Currently, different scholars and evaluation organizations at home and abroad conduct various evaluation and ranking activities on colleges and universities based on different recognition and purposes, however, the objective rationality of their evaluating methodologies and results is controversial. National Medium and Long-term Education Reform and Development Plan Outline (2010—2020) raises higher requirement for scientificalness of the evaluation on colleges and universities. On the basis of such four main functional indicators as scientific research, talent cultivation, reputation of a college or a university and school-run resources to construct evaluation indicator system for colleges and universities, this paper uses Delphi method to obtain data, then uses Analytic Hierarchy Process to make comprehensive evaluation on all kinds of colleges and universities of China and gets relatively scientific and objective evaluation results.