To analyze the relation between change of culture endowment and agricultural system innovation in China, the author points out that the contemporary resources endowment, technical and the institution change can cause the cultural endowment change. At the same time, the Cultural endowment change can forecast the institution transformation, especially in the agricultural aspect. To comment three important agricultural systems transformations which are led by culture endowment change, the author considers that there is a dynamic relation between culture endowment and agricultural system transformation that affects and restricts mutually. The author suggests three methods to optimize culture endowment and the agricultural system. Through these analysis, the author gives the conclusion that the Vicissitude of culture endowment can influence the farmers' mental and action, and it can further support the agricultural system evolvement.