There is little written history regarding Cheung Chau before the 18th century. But even early last century, some islanders said their families had settled on Cheung Chau hundreds of years ago, and we can guess something regarding the very early history based on some archaeological finds and the history of south China.
Fragments of pottery, shells and a bone arrowhead found at Po Yue Wan (near Sai Wan, in the southwest) show there were humans on Cheung Chau during the Late Neolihic - and (though dates are considered unreliable) perhaps as long as six thousand years ago. Indeed, as human relics have been found from 5000BC (and - at one site near Sai Kung - even from 35,000-39,000 years old), it's likely that people have been in the Cheung Chau area for 7000 years or more.
But in the earliest days, people may not have lived here all the time - as Cheung Chau was not yet an island. During the last ice age, there was so much water stored in ice sheets covering northern areas that sea level was over 100 metres lower than today, and there was a large coastal plain along what's now the south China coast. If you'd visited the Cheung Chau area then, you might have seen just two hilltops - the present north and south of the island - above valleys, and with other hills nearby.
After the ice age
As the ice age ended and the great ice sheets melted, sea level rose. The sea flooded in across the coastal plain, and in the Hong Kong area low valleys became inlets, hills cut off by the sea became islands, including Cheung Chau. As sea level stabilised around 4000 years ago, there were perhaps two islands at "Cheung Chau" - it was only later that currents swept gravel and sand between them to form the tombolo that's now the narrow land between the typhoon shelter and Tung Wan.
Perhaps because of a combination of coastal areas yielding some good archaeological sites, plus any forest peoples likely using implements and buildings that would mostly decompose without a trace, archaeologists consider Hong Kong's Neolithic inhabitants were mainly coastal residents. Fishing was evidently important: at one Hong Kong site, finds included fish bones and remains of large stingrays and sharks in the cultural layer.
The Hundred Yue - and the Tanka, Hoklo, Punti and Hakkas
By the Bronze Age, there were Chinese records telling of the "Hundred Yue" peoples in south China; these Yuet - or Yueh - were reportedly "barbarians", but perhaps that's at least partly a result of the victors being the ones who write history, as there are signs of south China people developing agriculture and having a rich culture. They were perhaps Austroasiatic, and said to be skilled navigators and fierce fighters.
After north China conquered the south during the Qin (221-207 BC) and Han (206 BC-AD 220) dynasties, there was surely some assimilation of the Yue by Han from the north, maybe giving rise to the Cantonese peoples, and the Tanka boat people (tho a Wikipedia article says the Tanka "arrived in Hong Kong around the 7-9th century from the Malay Oceanic" - perhaps wrong; also on Internet, there's info saying the Tanka came from mainland China, even suggestion they were descended from Mongols to become, "the Tankas; fine-looking men and pretty girls").
The Tanka - "egg people" - became the main boat people of Hong Kong, including Cheung Chau. Other peoples perhaps arrived, too.
Coastal Evacuation - and Massive Hardships
Though some families may indeed have been on Cheung Chau for centuries, it sems impossible they have been here throughout - for during the reign of K'ang Hsi, from 1662-1669, the coastline of southern and eastern China was foricibly evacuated. This was a measure to ensure the forces of the deposed Ming dynasty that had fled to Taiwan could not trouble the new, Qing dynasty.
The evacuation came immediately after grim times for the region, during the dying throes of the Ming. In the land that's now within the New Territories, one account noted 'The ground was covered with bones, in the day time nothing could be heard but the hum of flies, and at night the voice of weeping."
This was the worst period in Hong Kong's history - and Cheung Chau people surely suffered too. According to historian James Hayes:
"Whole communities were uprooted from their native place, deprived of their means of livelihood and compelled to settle where they could. The rural people risked their lives if they ignored the government edict to move, or ventured back into the prohibited area. It is recorded that about 16,000 persons from Hsin-an [the part of Guangdong including modern Hong Kong] were driven inland. Only 1,648 of those who left are said to have returned when the evacuation was rescinded in 1669 [it's not clear if this is all people, or men over 16]. The survivors' hardships did not end when they returned to take up their interrupted lives in their old homes, for it is recorded that destructive typhoons in 1669 and 1671 destroyed the new houses in many places. [For Tankas living in boats, in days before there was a typhoon shelter, and with no good weather forecasts, surely could have been major losses from typhoons stricking Cheung Chau.]"
Hoklos, Punti and Hakkas
Cheung Chau was eventually settled by peoples from several places in southern China - and though the island is tiny, even by last century they tended to live in distinct communities, even though there was some intermarrying.
Hoklos - chiefly fishermen, from eastern Guangdong and Fujian - were among the main early settlers, becoming fishermen and traders. Punti ("Belonging to this place" or "Natives of the soil" - Cantonese), Hakka ("Guest people" or "Strangers") and Chiu Chau (from eastern Guangdong) also moved in. At least some of these arrivals were likely prompted by hard times in mainland China, whether as others arrived from the north, and/or land quality declined making life harder.