With the increasingly prominent problem of agricultural non-point source pollution, the process of Rural Revitalization Strategy has been seriously affected. Studying the relationship between rural human capital and agricultural non-point source pollution is helpful to form talent bonus, improve rural ecological environment and realize the green development of agriculture. This paper takes 30 provinces and cities of China as the research object and uses Spatial Durbin model for empirical analysis. According to the research results, it is found that agricultural non-point source pollution has significant spatial correlation and the correlation presents a fluctuating trend; Rural human capital has obvious direct effect (-0.678) and spatial spillover effect (-0.707), which helps to alleviate agricultural non-point source pollution. After considering different forms of space matrix, the result is considered to be robust. The conclusion of this paper provides policy enlightenment for promoting the construction of rural human capital and improving the continuous development of rural ecological environment curriculum.