Maoli Lake is the water source for local residents and a national nature protected area. However, due to intensive agriculture development, the water quality has deteriorated over the past decades. An effective measure to improve water quality is to control the agricultural non-point source (NPS) pollution through elaborate schemes based on eco-compensation. In order to develop such eco-compensation schemes, three scenarios of agricultural activity adjustment were designed: S1 (halving fertilization every year), S2 (fallow every other year), and S3 (returning agricultural land to forest). A Soil and Water Assessment Tool (SWAT) model was adopted to simulate runoff, total nitrogen, and total phosphorus. Based on SWAT results, a multi-criteria spatial evaluation model considering the environmental, economic, and social effects of eco-compensation was created for best scenario decision. The results reveal the following: (1) the total nutrients loss of agricultural land reduces in all scenarios, but S2 has more reduction compared to S1 and S3; (2) from the comprehensive perspective of environment–economy–society effects, S2 is the best scenario for rice land and dry land; (3) the comprehensive effect of eco-compensation at the grid scale has a significant spatial difference, and therefore, we highlight the necessity and significance of controlling agricultural NPS pollution by eco-compensation on a precise spatial scale. This study can broaden the application field of the SWAT model and provide a scientific basis and experience for the evaluation and spatial design of agriculture eco-compensation.
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