The karst ecosystems of southwestern China are a global hotspot of cavefish diversity. To elucidate their evolutionary origins and diversification history, we analyzed 183 cave species and their close relatives from ten clades. Our findings reveal that freshwater fishes started colonizing caves ~44 million years ago (Ma). The primary driver of speciation was in situ diversification, which began around 43.8 Ma, increased sharply by ~25 Ma, and showed peaks at ~10 Ma and 2.4 Ma, with a valley at ~3.3 Ma. Distinct hydrological basins exhibited divergent diversification patterns. Dispersal from the Pearl River to the Yangtze River and vice versa began around 23.8 Ma and 12.6 Ma, accelerated at ~13 Ma and 8.2 Ma, and peaked at 16 Ma, 2 Ma, and 5 Ma, respectively. We propose that the river drainages of southwestern China developed stepwise from the late Eocene to early Pleistocene, with the Pearl and Yangtze River basins potentially establishing connectivity as early as the late Oligocene (~26 Ma) and undergoing repeated connections thereafter. The origin and diversification of cavefishes are intrinsically linked to the evolution of karst landscapes, shaped by orogeny and monsoon-driven climate changes since the late Eocene. These insights are crucial for informing the conservation of these unique karst habitats amidst ongoing climate change.