It has been confirmed that the karst rocky desertification (KRD) has severely changed the interactions between atmosphere and terrestrial ecosystem which would cause a significant effect on regional climate system. In this study, the Weather and Research Forecasting model was applied to investigate the biogeophysical impact on temperature and precipitation change by land use/land cover change data with different KRD conditions in 1993, 2003, and 2013 in Southwest China. The results showed that an improving trend of KRD has been found in Southwest China, especially in east Sichuan, Chungking, southwest Yunnan, and south Guangxi. The 2-m air temperature decreased by 0~− 1 °C in general with this improving trend. The possible reason was the decreasing KRD accompanied by the decreasing albedo, causing the increasing net shortwave radiation and the increasing net radiation. Meanwhile, the increasing evaporation strengthened the latent heat flux and weakened the sensible heat flux so that decreased temperature was addressed in forest areas. The effect of KRD change transferred to the upper troposphere through atmosphere vertical convection, which made the subtropical high to be strengthened and westerly extended. Therefore, the upward moisture flux at the surface (QFX) was weakened in the central part of Guangxi, southern Guizhou, which led to the decrease of the precipitation. Moreover, the southwest monsoon was strengthened, which caused the increasing water vapor flux and led to the heavy rainfall in the west of Yunnan.