This paper mainly conducts the research on the physical education teaching reform in Higher Vocational Colleges under the condition of independent recruitment in Anhui Province. The direction of reform in physical education includes: accelerating the elective courses teaching and the transformation of elective course system; improving the teaching conditions of higher vocational colleges actively; strengthening the construction of school-based teaching materials focus on the development and utilization of sports elective course project resources etc.. It is hoped that this paper can help to promote the reform of physical education in Higher Vocational Colleges under the condition of independent recruitment in Anhui Province by the writing of this paper.