Karst areas in southwest China have experienced significant land cover and land use change (LUCC) due to utilization for human activity and a comprehensive rocky desertification control project (RDCP) since 2008. It is important to quantify the effect of LUCC on ecosystem productivity in this region for assessing the overall benefit of this ecological restoration project. In this study, we used using MODIS land cover and NPP products to investigate the relative contribution of LUCC to the change in net primary productivity (NPP) during 2008–2013 in Huanjiang County, one of first one hundred pilot counties to implement RDCP. Our results show that NPP increased in 95.53% of the county, and the average growth of NPP in non-rocky desertification area was higher than in rocky desertification or potential rocky desertification areas. LUCC has an important contribution (25.23%) to the NPP increase in the county, especially in the LUCC area (70.97%), which increased the average NPP by 3.9% and 10.5%, respectively. Across the six RDCP regions in the county, the average increase in NPP for the vegetation restoration measure of governed karst area is significantly greater than in the ungoverned karst area, and the positive change in NPP increased with the increasing implementation area of the vegetation restoration measure.