Since "National Demonstrative Higher Vocational Colleges Construction Plan" was launched in 2005, the development of higher vocational colleges in China has been deeply embedded in the projectbased governance model. The projectbased governance model produces and reproduces the homogenization of higher vocational colleges through the legitimacy mechanism, and maintains the diversified development of higher vocational colleges through the residual control right formed by the "principalagent" relationship. Under the projectbased governance model, the homogeneous development of higher vocational colleges has many adverse effects, such as the inefficient allocation of central government resources and the lowquality involution of higher vocational colleges; the tension between the national demand, local demand and industry demand; the nonacclimatization of achievement promotion and the lack of motivation of practical innovation. In order to solve the problem of homogeneous development, the future projectbased governance of higher vocational colleges in China should focus on improving the central government project application mechanism and clarifying the functional orientation of central government projects and local government projects; piloting the project application model of "mandatory + optional" to promote the development of classified characteristics of vocational higher education; implementing the evaluation model of "basic performance + typical results" and improving the evaluation weight of multiple subjects; strengthening the dynamic guidance on project implementation and gradually improving the policy clarity.