With the continuously expansion of functions and scope of services of higher education self-study examination, the management of self-study examination is more and more difficult and new problems emerge. How to make self-study examination of higher education adapt to the requirement of application-oriented talents is a key problem, and an innovative management system is a key step. The management status and problems of self-study examination of higher education were studied, and some suggestions for management system innovation were proposed which can provide a reference for healthy and sustainable development of self-study examination management in higher education.