With the accelerated operation of subway networks, the increasing number of subway transfer stations results in inefficient passenger travel. The target of this paper is to solve the research question of how to reduce transfer waiting time (TWTT) for heterogeneous passengers. The key problem is to determine the optimal concerted train timetable considering the transfer walking time (TWKT) of the passengers. On the basis of field survey data, the regression method was used to establish a TWKT prediction model for general passengers (G) and vulnerable passengers (V), including the elderly, passengers traveling with children, and those carrying large luggage. Afterward, a two-objective integer programming model was formulated to minimize the subway operating costs and TWTT for each group, in which V is given the priority weight to ensure social equity. The headway, loading capacity, and TWKT of heterogeneous passengers were set as optimization model constraints. A genetic algorithm (GA) was designed to find the optimal solution. A case study in which the Beijing Jianguomen Station was selected as the key transfer station was conducted to verify the performance of the proposed model. Key results show that the total TWTT for V and G can be reduced by 18.6% and 27.2%, respectively, with one train saved. Results of the parameter sensitivity analysis reveal the interconnection between the operating cost, heterogeneous passenger proportion, and transfer time. The proposed model can be used for improving transfer efficiency for passengers while considering the enterprise operating costs.