In this study, it was the first time that genetic diversity and differentiation pattern of Actinidia chinensis populations across the species native range in China were investigated on 12 nuclear microsatellite markers. Effect of environment in these mountains on the pattern was also explored. Qinling Mountains was shown to have the highest genetic diversity in the A. chinensis. By contrast, the lowest genetic diversity of the species was confirmed in Nanling Mountains. The highest differentiation was observed between populations in Qinling and Nanling, while the least differentiation was observed between populations from Wuling and Luoxiao Mountains. The diploid var. chinensis populations were clustered into 4 ancestral groups. Strong structure of diploid var. chinensis was confirmed by the single ΔK peak, while different ΔK peaks for hexaploid var. deliciosa suggested a weak structure. Stepwise regression analysis was also conducted between alleles and bioclimatic variables. Isothermality (Bio3) and precipitation seasonality (Bio15) significantly affect variation in most of the alleles. UDK96-001, Ke129, and Ke209 were found to have a higher number (>50 loci) of loci significantly associated with the bioclimatic variables. We suggest three dispersal routes for A. chinensis population based on present data and chloroplast data: (1) the relic population dispersal from Wuyi Mountains to Huangshan and Tianmu Mountains, across Baba Mountains, finally reach Qinling Mountains; (2) the populations dispersal from Wuyi Mountains to Luoxiao Mountains, then go into Nanling and Xuefeng Mountains, afterwards, one expands to Wuling Mountains and arrives to Daba and Qinling Mountains; (3) one branch of 2 goes into Yungui Plateau and finally arrives to Hengduan Mountains. Our results also provide fundamental genetic information for conservation of the species germplasm to improve the genetic basis for breeding its cultivars.