This study is dedicated to exploring the construction and implementation of innovation and entrepreneurship education system in higher vocational colleges. By analyzing the relationship between education investment and industrial employment, it further enhances the innovation and entrepreneurship ability of students in higher vocational colleges. It promotes the synergistic development of education and economy. First, the relationship between higher education investment and industrial employment is analyzed by VAR model, which reveals the influence of education on the structural adjustment of industrial jobs. Second, the evaluation indexes and quality clustering of innovation and entrepreneurship education are refined through fuzzy cluster analysis and K-means clustering method based on seagull optimization algorithm. The research results show that the improved innovation and entrepreneurship education system can significantly improve students’ innovation and entrepreneurship satisfaction and self-evaluation, in which the indicators of entrepreneurial spirit and psychological quality are considerably enhanced. In addition, students’ innovation and entrepreneurship ability showed significant differences in multiple dimensions. This study confirms the effectiveness of the construction of innovation and entrepreneurship education system in higher vocational colleges, which is substantial in improving students’ innovation and entrepreneurship ability.