The conversion of independent colleges is a major task for higher education reform during the “14th Five-Year Plan” period. In reality, this conversion is exposed to a number of risks. Categorizing risk types, evaluating risk levels and working out preventive measures are of top priority in the process. The conversion involves multiple interests. Most of the studies in the past were qualitative analysis, and there was hardly any quantitative study. Therefore, selecting representative indicators through the analytic hierarchy process from five dimensions, i.e., legal policy risk, social stability risk, education and teaching risk, political security risk, and financial asset risk, this paper constructs an evaluation index system for the prevention of the risks in the conversion of independent colleges. It is very important to construct a systematic risk evaluation index system for the conversion of independent colleges through the fuzzy comprehensive evaluation method to evaluate the risk level of the conversion of state-owned privately-run independent colleges and privately-owned privately-run independent colleges. It is found that, on the whole, the risk of the conversion of the state-owned privately-run independent colleges is slightly higher than that of the privately-owned privately-run independent colleges. In view of the potential risks, it is necessary to improve the risk prevention mechanism for the conversion of independent colleges through the following means: adapting measures to local conditions in accordance with laws and regulations; improving the risk prevention leading mechanism; making risk assessment; improving risk mitigation and response mechanism.