Nowadays malaria still is a significant and prevalent infectious disease in mainland China. How meteorological and socio-economic factors affect the distribution of malaria in mainland China? It is worthy to explore their impact on malaria to guide other serious regions. This study selects the total number of malaria cases included in both local and imported cases of malaria in mainland China from 2006 to 2015. According to integrating 6 meteorological and socio-economic factors, we use the spatiotemporal analysis and Bayesian model to quantify the impact of multi-factors on malaria. The results show that malaria is distributed in a northeast southwest direction, with hotspots mainly located in Shandong, Anhui, Jiangsu etc. Precipitation has a significant impact on the incidence of malaria, while socio-economic factors have no significant impact on the incidence of malaria. In addition, malaria in mainland China exhibits significant spatial heterogeneity, with significant differences in RR(Relative Risk) of different regions. The related results aim to provide the theoretical guidance for formulating the prevention and control policy.