Abstract:The establishment of enterprises as the mainstay of commercial breeding mechanism is the inevitable choice of China's seed industry modernization, and the science- Enterprise Cooperation implementation mechanism is the key to achieve commercial crop seed breeding industry. Based on the synergetics theory, this paper constructs the theoretical research frame of cooperation mechanism of seed industry cooperation, and uses 433 survey data of 48 science and education units in 6 provinces of western China, and applies logistic binary choice model to analyze the present situation of cooperation and the degree of influence of cooperation mechanism elements on the participation and cooperation of science and education units. In addition, The empirical study shows that the the key to improve the cooperation mechanism is to strengthen the depth of cooperation, realize the clarity of the cooperative system and guide and support the external environment.