Nowadays, facing toward the entrepreneurial Universities and optimal performance in entrepreneurial higher education system is the main strategy in agricultural higher education system. In this regard, the main of this study was to analyze the effectiveness of agricultural higher education system on improvement of entrepreneurial capabilities among agricultural students (M.Sc. and PhD levels). By using of stratified random sampling method, among graduate students of agriculture in University of Mohaghegh Ardabili (N=995), sample size of 288 was determined. The research instrument consisting of standardized test "to measure personality traits of entrepreneurship in Iran" with standardized international test of entrepreneurship center of Durham University in England and five variables of the effectiveness of entrepreneurial higher education system. The results showed that the majority of respondents, in terms of achievement motivation and internal control were "relatively high" level; but in terms of independence, risk taking and creativity were at "relatively low" and "low" levels, respectively. Other findings suggest that only there was significant difference between two abilities of independence and risk taking, among M.Sc. and PhD students. Also, the upper GPA among respondents has increased their achievement motivation; but the increase in GPA, has not made a significant impact on entrepreneurial capabilities. According to regression analysis, totally, three variables of content and curriculum (Beta= 0.392), management and infrastructure factors (Beta= 0.304) and methods of teaching and training (Beta= 0.229) explained 60.2 percent of factors affecting on improvement of entrepreneurial capabilities among respondents. Therefore, the priority of educational planning to enhance the independence, risk taking and creativity of students in the three effective variables will be effective in improving the effectiveness of the agricultural education system.