Mutual recognition through security checks can improve the transfer efficiency and service level between different modes of transportation, especially for large hub high-speed rail stations. Implementing a reasonable mutual recognition plan through security checks is more conducive to improving the integration of transportation and travel. In order to analyze and quantify the influencing factors of the transfer efficiency between large-scale high-speed rail hub stations, aviation and subway, the explicit and hidden cost input in the transfer was analyzed, and the input indicators covering economic from the perspective of resource input and benefit output, which manpower and management were selected and the advantages and disadvantages of the implementation of mutual recognition of security checks on stations and passengers were projected into specific indicators, and output indicators containing expected and undesired outputs were obtained so as to construct an evaluation system for the efficiency of the security inspection mutual recognition program. In order to form a complete system of different security mutual recognition schemes, the basic processes were delineated, and four basic security mutual recognition transfer flow lines were ultimately obtained. Based on the characteristics of this problem and the multi input and multi output indicator system, an SBM evaluation model was established. Finally, taking the transfer between Lanzhou West Railway Station, Zhongchuan airport and Lanzhou rail transit as an example, the mutual recognition scheme of security inspection is assumed, and the index system and model are applied for evaluation and analysis. The results show that: the one-way inspection exemption from Zhongchuan airport to Lanzhou West Railway Station, and the one-way and two-way inspection exemption between Lanzhou West Railway Station and rail transit are all effective input-output schemes. Through the comparative analysis of the input-output levels of the three effective schemes, the decision-making suggestions and references are given from the perspective of minimum cost control, minimum unexpected output and maximum economic benefits of the station.