The quality of higher education is an essential factor that relates to the long-term development of school’s infrastructure, it is also the main target for education reform, because all education activities were done with the education quality as the center. With the situation of increasing demand for high quality talents in our society, the scale of higher education has increased gradually, how to maintain the high quality and high level of higher education has become an urgent problem for ensuring the effectiveness of education. This paper based on EFQM model, combing with some constitute elements such as education content, responsibility allocation, management mode, resource distribution, research result and analysis improvement, analyzing the function need and performance requirement of the higher education quality assurance system, and designing of the system’s general framework and process, constructing the model of higher education quality assurance system and assessing the system’s effectiveness and feasibility. This system comprehensively considers the complexity and practicality of the higher education, which has provided a powerful evaluation tool for effectiveness analysis of this design process. Study and analysis in this paper has proved the effectiveness of the higher education quality assurance system based on EFQM model as well as its flexibility and practicality, which can be used in our country’s higher education quality assurance system, by which can give direction for education system reform and provide measures, in this way it can provide more high-quality talents which are conducive for national and social development.