At present, the secondary security check at the transfer station between high-speed railway and urban rail transit brings inconvenience to passengers. The aim of this study is to develop a methodology for evaluating the safety level of high-speed railway and subway stations by using variable fuzzy set theory, so as to determine the conditions for security check mutual recognition. In this research, considering transportation capacity, personnel and equipment, and environment and management, three aspects are considered to construct an evaluation index system for mutual recognition of high-speed railway and urban rail transit security check. Then, the variable fuzzy safety evaluation model has been established for high-speed railway and subway stations and their transport modes to analyse the feasibility of security check mutual recognition. Using the variable fuzzy set theory and the important consistency sorting theorem, the decision approach proposed in this study was tested for the high-speed rail station A and subway station B. As a result of using the methodology, the safety evaluation result of high-speed railway station A is 1.60, and the result of subway station B is 2.26. It is concluded that the safety of high-speed rail station A is higher than that of subway station B, and it is possible to enter the metro station without security check in one direction. The approach presented in this research can be used for judging the conditions for security check mutual recognition at interchange stations between high-speed railway and urban rail transit, which provides reference for the implementation of security check mutual recognition.