With the development of application-oriented universities and colleges, innovation and entrepreneurship education reform and personnel training have attracted much attention. Education quality evaluation is an important means of promoting the development of innovation and entrepreneurship education, there are still some problems such as unclear goal, backward idea, single method and so on. By combing the present situation of the evaluation of innovative entrepreneurship education in application-oriented universities and colleges, we find out the problems and probe into the reasons, from the aspects of goal orientation, teaching process, teaching staff, service guarantee and training effect, the evaluation indexes are scientifically formulated, the quality standard of innovative entrepreneurship education is clearly defined, and the measures and methods of quality evaluation are improved, promoting the quality of innovative and pioneering education in application-oriented universities and colleges.