In view of the phenomena of using the same standard comprehensive evaluation to all students in the current university, not considering the difference of individual special ability of the students, and avoiding to produce the phenomenon of high grade and low ability of the students, the rough set theory and the average evaluation method were used to find out the weak link of students' ability and to enhance students' ability of different quantization. The experiments showed that the students' comprehensive ability could be evaluated by the rough set theory, which also provided theoretical basis for the students to improve their comprehensive quality and ability.