Abstract: Nowadays, the actual legal system of ecological agriculture has not been established in China. Existing legal guarantee measure depends on ecological environment protection legal system which based on natural resources protection and pollution prevention. Based on summarization of ecological agriculture system, it accurately analyzes several obstacles existed of ecological agriculture legal system in ideology domain, social structure, law guide and so on. At last, in order to improve the legislation process of ecological agriculture, it proposes several law countermeasures for how to eliminate the obstacles of ecological agriculture system from several sides, such as clearing ecological agriculture essence further, expediting legislation matching with ecological agriculture, strengthening local legislation.