The construction of a Y-type urban rail transit line can effectively solve the problems of low line coverage and low utilization in suburban areas. The purpose of this paper is to study and analyze the effect of different operation modes of the Y-type line of suburban urban rail transit. In this paper, the objective function is to minimize value of passenger travel time costs and enterprise operating costs, and the main and branch train frequencies are used as decision variables to establish a selection model for Y-type operation mode, and design an improved multi-objective optimization algorithm based on NSGA-II. A case study was carried out on the Y-type line to evaluate the effect of each scheme. The results of the study found that there is no obvious difference between the advantages and disadvantages of the three operation modes. The passenger waiting time under the independent operation plan is the highest but the comfort level is greater, and the train travel distance is the lowest. The partial- through operation accommodates the interests of both passenger and business. Therefore, the corresponding operating mode should be selected according to the preferences of passengers and enterprises.