We construct a comprehensive analysis framework of population flow in China. To do so, we take prefecture-level administrative regions as the basic research unit of population flow and use source-sink theory and flow space theory. Additionally, we reveal the dynamic differentiation of population flow patterns and the evolution of population source-flow-sink systems. We try to provide a theoretical basis for the formulation of population development policies and regional spatial governance. The results show the following: (1) The Hu Huanyong Line has a strong spatial lock-in effect on population flow. Additionally, provincial capital cities, headed by Hangzhou, Nanjing, and Hefei, have played an increasingly prominent role in population flow. (2) The developed eastern coastal areas have undertaken China’s main population outflow. The net population flow is spatially high in the middle of the region and low on the two sides, exhibiting an “inverted U-shaped” pattern. Furthermore, the borders of the central provinces form a continuous population inflow area. (3) The hierarchical characteristics of the population flow network are obvious. Strong connections occur between developed cities, and the effect of distance attenuation is weakened. The medium connection network is consistent with the traffic skeleton, and population flow exhibits a strong “bypass effect”. (4) The source and sink areas are divided into four regions similar to China’s three major economic belts. The 10 regions can be refined to identify the main population source and sink regions, and the 18 regions can basically reflect China’s level of urbanization. The network of the population flow source-flow-sink system exhibits notable nesting characteristics. As a result, it creates a situation in which the source areas on both sides of the east and the west are convective to the middle. The hierarchical differentiation of the source-flow sink system is related to the differences between the east and the west and between the north and the south, as well as local differences in China.