The karst area in Yunnan-Guangxi-Guizhou region in southwest China is known for widespread rocky desertification but several studies report a greening trend since the year 2000. While the start of the greening trend seems to match with the implementation of ecological conservation projects, no statistical evidence on a relationship between vegetation greening and eco-engineering exists. Moreover, dominant factors influencing the spatial patterns of vegetation trends have rarely been investigated. Here we use six comprehensive factors representing the natural conditions and human activities of the study area, and several statistical models consistently show that eco-engineering explains large parts of the positive vegetation trends in the karst areas, while negative vegetation trends in non-karst areas of Yunnan were related with a decrease in rainfall. We further show that the interaction of eco-engineering with other factors leads to a heterogeneous pattern of different vegetation trends. Knowing and understanding these patterns is crucial when planning ecological restoration, especially in diverse landscapes like China karst and the methods can be reused in other restoration areas.