The construction of dual prevention mechanism is a necessary way to solve the problem of “not recognizing, not thinking, not managing well” in the field of enterprise safety production. This paper combines the elements involved in the theoretical framework of the dual prevention mechanism, constructs two evaluation index systems of safety risk classification and the operation effect of the dual prevention mechanism, and then establishes an evaluation model based on the multi-level analysis method and the fuzzy comprehensive evaluation method, to explore the operation effect of the dual prevention mechanism in the enterprise. The evaluation results show that after the dual prevention mechanism of safety risk classification and hidden danger investigation and management strategy is operated in S enterprises with higher safety risk level (1.50 points), the awareness of safety production and the level of intrinsic safety of the enterprises have been significantly improved, and the average value of the evaluation of the operation effect of the dual prevention mechanism in enterprises is 3.91 points, which reaches a good level. The research results of this paper not only have strong guiding significance and practical help for the optimization of risk management of production safety in enterprises, but also can be used by the same type of enterprises and even other enterprises in optimizing the risk management of production safety and the management of hidden danger investigation.