The purpose is to analyze the economic development and management mechanism of rural enterprises, and explore the role of ecological environment protection mechanism in the economic development of rural enterprises. First, the related theories are analyzed and expounded; then, the participants of rural enterprise economy are analyzed, and the evaluation index system of rural enterprise economy is established. The economic and management mechanism of rural enterprises under the ecological environment protection mechanism is analyzed by using the model projection pursuit evaluation model under the real coded accelerated genetic algorithm. The results show that the ecological index coefficients are 0.0856, 0.1334, 0.1977, 0.2123 and 0.2543 respectively. In addition, the ecological economic index are 0.1932, 0.2168, 0.2693, 0.2168 and 0.1933. Irrigation level, effective control of soil erosion rate and forest coverage exert a significant impact on the economic development and management mechanism of rural enterprises; the small per capita water resources index indicates that it is essential to improve the water cycle; the occurrence rate of agricultural natural disasters exerts little influence on the development of agricultural circular economy, indicating that the ability of agriculture to resist natural disasters still needs to be improved. To sum up, this exploration can provide reference for the sustainable development of rural enterprise economy.