Yunkaidashan, located at the southern South China block (SCB) and closely adjacent to the Indochina block, is an ideal region for better understanding the temporal and spatial framework of tectonothermal overprinting at the southern SCB since Mesozoic. Apatite and zircon fission track thermochronology of various-type rocks from Yunkaidashan is presented in this paper. The results show, no matter what rocks are, the apparent ages of zircon fission track range from 97.4 to 133.0 Ma, and those of apatite fission track from 43.2 to 68.4 Ma. The length of apatite fission track yields an average confined track length of ～13 μm and shows normal distribution of unimodal frequency. It is inferred that the uplifting amplitude has been more than 5 km in Yunkaidashan since late Mesozoic. The difference of fission track apparent ages at different locations in Yunkaidashan suggests a paleophysiognomic scenario of the heterogeneous uplift/denudation. These data of the fission track thermochronology provide new constraints for better understanding the tectonophysiognomic pattern of the SCB since late Mesozoic.