With the continuous development of the times, the transformation and reform of higher education has brought many problems. In this paper, we carry out research on the transformation of higher education, put forward the educational reform path based on the theory of organizational experiment, improve the higher education management model based on the three-dimensional integration, and construct the campus education management system based on the multilayer network by combining with the needs of campus management. On this basis, an evaluation model oriented to multilayer network is established by using association matrix and probabilistic transformation, which is utilized to evaluate the system, and comparative education management experiments are designed to test the application effect of the constructed system. In this paper, the response time of the educational management system using multilayer network is 0.35~0.80s, which is about 0.45s faster than that of the traditional system, and about 0.26s faster than that of the single-layer network controller. The students using this educational management system have improved their interest cultivation, innovation ability, cooperation ability, and scientific attitudes in comparison with the pre-application ones, which are 3.534, 2.452, 2.721, and 2.51, respectively, 2.721 and 2.51.The higher education management model proposed in this paper can have the ability to improve students’ competence level and provides an effective path for the reform of higher education management.