Since the implementation of China’s afforestation and conservation projects during recent decades, an increasing number of studies have reported greening trends in the karst regions of southwest China using coarse-resolution satellite imagery, but small-scale changes in the heterogenous landscapes remain largely unknown. Focusing on two typical karst regions in the Nandong and Xiaojiang watersheds in Yunnan province, we processed 2,497 Landsat scenes from 1988 to 2016 using the Google Earth Engine cloud platform and analyzed vegetation trends and associated drivers. We found that both watersheds experienced significant increasing trends in annual fractional vegetation cover, at a rate of 0.0027 year−1 and 0.0020 year−1, respectively. Notably, the greening trends have been intensifying during the conservation period (2001–2016) even under unfavorable climate conditions. Human-induced ecological engineering was the primary factor for the increased greenness. Moreover, vegetation change responded differently to variations in topographic gradients and lithological types. Relatively more vegetation recovery was found in regions with moderate slopes and elevation, and pure limestone, limestone and dolomite interbedded layer as well as impure carbonate rocks than non-karst rocks. Partial correlation analysis of vegetation trends and temperature and precipitation trends suggested that climate change played a minor role in vegetation recovery. Our findings contribute to an improved understanding of the mechanisms behind vegetation changes in karst areas and may provide scientific supports for local afforestation and conservation policies.