Long queues formed at the Hong Kong international airport's check-in counters for flights to mainland cities including Beijing, Tianjin and Xiamen.
Hong Kong media outlets estimated that thousands were crossing.
Beijing has quotas on the number of people who can travel between Hong Kong and China each day.
I'm thrilled, I can't believe it’s happening,” said a businesswoman surnamed Shen, 55, who flew in from Hong Kong.
The World Health Organisation said on Wednesday that China's COVID data underrepresents the number of hospitalisations and deaths from the disease.