China's economic recovery relies on the coordination between the pandemic control and socioeconomic development. Based on the Baidu migration big data, this study employs difference-in-difference model to explore the impacts of pandemic prevention and control measures on the population flow at different stages. The results show that the unconventional measures proposed in the early stage have effectively controlled the population flow, with the average intensity of urban population inflow, outflow and intra-city flow reduced by 71.21%, 72.62%, and 45.99% respectively. After the resumption of work and production, the population flow began to rebound, with the inter-city flow more than doubled. The pandemic risk level is a vital factor affecting the resumption of population flow in China. Therefore, differentiated accurate prevention and control measures should be adopted to create favorable conditions for promoting economic development in the era of regular pandemic prevention and control.