Geographic features play an important role in shaping the phylogeographic structures of species. Salvia miltiorrhiza Bunge is a widely studied medicinal crop. In this study, we used three cpDNA sequences (trnL–trnF, atpB–rbcL, and rpl16) to investigate the phylogeographic structure and evolutionary history of 190 S. miltiorrhiza endemic plants taken from 11 locations in the Qinling, Dabie, and Mengshan Mountains of Central China. Fifty-three total haplotypes were identified, and 50 of these were population-specific. In addition, moderate-to-high genetic differentiation was observed among the populations (mean Fst = 0.325), while phylogeographic structure was also observed based on STRUCTURE and spatial analysis of molecular variance (SAMOVA) analyses. In addition, BEAST and DIYABC analyses suggested that divergence times of the haplotypes in the AHS and ALQ2 populations of the Dabie Mountains were earlier than those in the Qinling and Mengshan Mountains. Consequently, an evolutionary scenario of S. miltiorrhiza populations in the Qinling and Mengshan Mountains diverging from populations in the Dabie Mountains was highly supported. The results reported here provide a useful framework for understanding the role of geographic features in shaping the spatial genetic variation and evolutionary history of S. miltiorrhiza plants.