Objective To explore whether the spatial autocorrelation exists in the incidence of HIV/AIDS in Chongqing, discuss features of the spatial distribution, and analyze the trend of variation with time for hot regions. Methods The annual incidence of HIV/AIDS of districts and counties of Chongqing from 2004 to 2012 were calculated and the global spatial autocorrelation analysis and the local spatial autocorrelation analysis were conducted. Results The annual global Moran's I indexes from 2004 to 2012 were larger than 0 (P<0.05), which indicated that positive spatial autocorrelation existed in the data. Results of the LISA analysis showed that the cluster state was high-high or low-low. Results of the G*i analysis indicated that the hot regions expanded with time. Conclusion The significant positive correlation exists in the spatial distribution of incidence of HIV/AIDS in Chongqing from 2004 to 2012. Hot regions expand with time, which indicates that the prevention and health care of HIV/AIDS in Chongqing should be reinforced.