Abstract: Autonomous enrollment policy in universities has been the concern of society since it was approved by the Ministry of Education in 2003. There are inequity existing between students from key high schools and common high schools, from highquality base schools and nonones, from urban and rural areas from the aspect of qualification. In evaluation process, fairness can not be guaranteed due to ambiguous conditions and undefined procedures. And inequity appears among students from different areas and between liberal arts and sciences. The author suggests that autonomous enrollment reform should start from the qualification examination, and ensure equal opportunity to students from the very beginning. Scientific and transparent procedure of autonomous enrollment policy should be adopted to guarantee the process equity. Qualification policies should be formed according to education status in different areas. The supervision branch should play the role in guaranteeing the fairness in autonomous enrollment.