The COVID-19 epidemic has become a Public Health Emergency of International Concern . Thus, this sudden health incident has brought great risk and pressure to the city with dense population flow . A deep understanding of the migration characteristics and laws of the urban population in China will play a very positive role in the prevention and control of the epidemic situation . Based on Baidu location-based service (LBS) big data, using complex networks method and geographic visualization tools, this paper explores the spatial structure evolution of population flow network (PFN) in 368 cities of China under different traffic control situations . Effective distance models and linear regression models were established to analyze how the population flow across cities affects the spread of the epidemic . Our findings show that: (1) the scope of population flow is closely related to the administrative level of the city and the traffic control policies in various cities which adjust with the epidemic situation; The PFN mainly presents the hierarchical structure dominated by the urban hierarchy and the regional isolation structure adjacent to the geographical location . (2) through the analysis network topology structure of PFN, it is found that only the first stage has a large clustering coefficient and a relatively short average path length, which conforms to the characteristics of small world network . The epidemic situation has a great impact on the network topology in other stages, and the network structure tends to be centralized . (3) The overall migration scale of the whole country decreased by 36.85% compared with the same period of last year's lunar calendar, and a further reduction of 78.52% in the nationwide traffic control stage after the festival . (4) Finally, based on the comparison of the effective distance and the spatial distance from the Wuhan to other destination cities, it is demonstrated that there is a higher correlation between the effective distance and the epidemic spread both in Hubei province and the whole country.