AIDS is a kind of serious infectious disease which seriously endangers human health. With the increase of global mobility, the speed of the spatial spreading is faster and faster in China. The cross-region flow of China’s population continues to increase, and the speed continues to accelerate. In this context, spatial auto-correlation, convergence test and principal component regression were used to investigate the spatial and temporal changes of new AIDS epidemics and its relationship with population mobility in China from 2004 to 2014 in this paper. The basic data used in the study came from “The direct online reporting system of National infectious disease and public health emergency network” and other authoritative information published by other government departments. The research indicates: 1) Since 2004, the annual number and incidence of new AIDS incidences grew rapidly. Based on the number of incidence and morbidity, the epidemic level of each province was divided into four grades, they were low, moderate, higher and highest grade. It was found that the level of new AIDS epidemic in China showed the spatial distribution pattern, namely “high in the south, low in the north, high in the west, low in the west”. From the perspective of the average annual growth rate of each province, the change of the new epidemic not only showed the obvious growth at the provincial level, but also showed the “fastest in the west, fast in the east, the lowest in the central part” in the three zones. 2) There is a spatial auto-correlation phenomenon in the new AIDS epidemic situation in each province, which is influenced by the incidence level of adjacent areas, and the trend of geographical agglomeration is obvious. In the southwest region, it formed a high incidence zone which centered Guangxi, Yunnan and Guizhou. In the northwest, northeast and other places, it formed low-incidence closely grouped area. AIDS epidemic distribution has a strong spatial correlation, which was related to the continual improvement of marketization in China and the social-economic factors flow among different provinces, especially the continuous increase in population mobility. 3) The temporal and spatial changes of the incidence of newly diagnosed AIDS in each province showed the trend of convergence, indicating that the increase rate in the lower initial level of the epidemic will be faster than the initial high level, and the growth rate in the initial higher level was slower than that in the lower area. And in that case, the difference will reduce between the two regions, and are expected to gradually converge to a higher level. However, there is no trend of convergence towards provincial difference in the incidence of new AIDS. 4) Under the condition of controlling the regional economic level and medical resource endowment, the intensity of regional population movement and the new epidemic change, the regional outflow and the increase of the population will promote the increase of the incidence level. In order to effectively eradicate the transmission of AIDS and cut off the transmission chain, the government should also consider optimizing the current prevention and control system from the perspective of improving the management of population flow the policy of “preventing first, combining prevention and treatment, comprehensive management”. Whether it is in the outflow or inflow provinces, it should strengthen the propaganda and education on HIV/AIDS prevention and establish the mechanism in mutual-controlling work of inflow and outflow areas.