The development of new colleges has been mentioned frequently and attracted more attention. However, as to what kinds of colleges need transformation and how to do it, the researches are still at the theoretical level. This paper constructs university scientific research competitiveness index system, by collecting relevant data and using the analytic hierarchy process combined with super efficiency DEA, to point out what colleges need transition. Compared with colleges which were upgraded from junior colleges to university since 1999, it is found that the consistent rate of the final results is 89.74%. This proves the rationality of the results obtained in this paper. At last, this paper puts forward some suggestions on how to transform specifically.