In recent years, China’s economy has developed rapidly; many small companies have risen rapidly; and the tax system has become more and more standardized. Because many small businesses cannot afford to hire full-time accountants, they opt to outsource accounting services, giving small- and medium-sized bookkeeping firms a large market space. However, these opportunities also bring huge operational risks to small- and medium-sized bookkeeping companies. The purpose of this research is to help such enterprises carry out risk management and reduce operational risks. This study uses an analytic hierarchy process and a fuzzy comprehensive assessment approach to successfully combine quantitative and qualitative analysis and create a multilevel analysis structure model of the risk management evaluation index system of small- and medium-sized agency accounting firms. The structural model is verified by a case, the specific risk score of each factor is calculated through the scores of 20 experts, and the importance of risk is judged according to the size of the score, indicating that the structural model is feasible.