Innovation and entrepreneurship education is an important carrier to stimulate higher vocational students’ innovative spirit, and entrepreneurial enthusiasm and enhance vocational students’ professional quality and professional spirit. This paper analyzes the problems and challenges of the integration of innovation and entrepreneurship education and professional education in higher vocational colleges from three aspects: value connotation, innovation and entrepreneurship education system and practical teaching base. Based on the current innovation and entrepreneurship education reform practice in some higher vocational colleges, this paper puts forward the practical path of the integration of innovation and entrepreneurship education and professional education in higher vocational colleges, which provides a reference for the innovation and entrepreneurship education reform in higher vocational colleges.