The benefit compensation of main grain producing areas includes not only the traditional feedback compensation, but also the endogenous benefit compensation mechanism which can improve the self-development ability. Based on data of 283 farmers in 11 main grain producing areas(counties) of Anhui province, this paper analyzes the influencing factors of the compensation mechanism of the inherent benefits in the main grain producing areas of Anhui province by structural equation model. It is found that reprocessing of grain products, brand cultivation of characteristic agricultural products, encouraging innovation mechanism, agricultural professional cooperatives and logistics distribution of agricultural products have direct effects on endogenous benefit compensation mechanism, while grain subsidies, grain prices, agricultural prices, grain output, farmland water conservancy construction and ecological environment protection have indirect effects on endogenous benefit compensation mechanism. New rural cooperative insurance, new rural cooperative medical care and minimum living security have little effect on the compensation mechanism of endogenous benefits.