To systematically evaluate the pollution control effect of the integrated protection and restoration conservation of mountain, river, forest, farmland, lake, grassland, and desert ecosystems in the typical karst basin, 18 typical ecological restoration projects in Lijiang River basin in Guangxi were monitored and evaluated for 10 months. The research shows that the overall water quality of the basin presents the spatial pattern of “excellent upstream, urban deterioration and improvement of restoration area” and the seasonal characteristics of “double peaks” of non-point source pollution accumulation in wet season and point source pollution accumulation in dry season; the upstream and downstream correlation analysis reveals the “channel effect” and “decoupling effect” of the engineering action mechanism; organic pollution from domestic sources and nutrient pollution from agriculture and endogenous sources are the two main controlling factors affecting the water quality difference in river basins. This study holds that the ecological restoration project in Lijiang River Basin has significantly improved the overall water quality, but its efficiency is jointly restricted by the project type, spatial location and external pollution load, and puts forward corresponding measures to improve the water environment quality in the future.