Savanna-like vegetation and dry thickets occur in hot dry valleys across southwestern China. Here, the flora and biogeography in hot dry valleys with savanna-like vegetation in SW China are studied. Native seed plants of 3217 species and varieties from 1038 genera in 163 families are recorded from these hot dry valleys. The biogeographical elements with a tropical distribution contribute 57.18%, but the ones with a temperate distribution contribute 36.45% of the total genera of the flora. This implies that the flora in hot dry valleys is of tropical margin nature and has been influenced by temperate elements. Floristic divergence across these hot dry valleys is obvious. The floras in the Yuanjiang and the Nujiang valleys are dominated by tropical elements (with a tropical distribution) (77.26% and 74.49 of the total genera, respectively), but the flora of the Jinshajiang valley is composed of half tropical (47.27%) and half temperate (44.96%) genera. Regarding floristic similarities, the Jinshajiang shows the highest similarity to the Yuanjiang although these river valleys are located a great distance from each other. We hypothesize the geological events in Yunnan could profoundly influence the flora and its divergence of the savanna-like vegetation in these deep, hot dry river valleys. Our results could be well explained from the geological events since the Cenozoic, such as the uplift of Himalayas, the extrusion of Indochina, the river capture of the Jinshajiang separating from the Yuanjiang, and the northward movement of the Burma Plate. Our study could be clues to explore the possible formation of the savanna-like vegetation.