For intercity railway transportation enterprises, a reasonable intercity train operation plan is not only the foundation of the intercity railway operation organization, but also the key to the sustainable development of the intercity railway (ICR). In this paper, taking into account the economic benefits of railway transportation enterprises and the social benefits of passenger travel, an optimization model is established with the intercity railway train operation plan as the research object. The model aims to minimize the operating cost of railway transportation enterprises and minimize the travel time of passengers, and considers constraints such as passenger seat utilization, passenger flow, train frequency, and stops. It is a multi-objective optimization model that accumulates two objectives by introducing the passenger time value coefficient. According to the characteristics of the model, a genetic algorithm is designed to solve the model. Taking the Beijing-Xiong’an Intercity Railway (BXICR) as an example, the “smart business card” of China’s high-speed railway, two scenarios of passenger time value are designed, and the optimized train operation plan is obtained according to the existing OD passenger flow data, which verifies the effectiveness of the model and algorithm. The results show that compared with the original train operation plan, the number of stops per train of the optimized train operation plan under the two passenger time value scenarios decreased by 8.8% and 14.9%, the operating cost of the enterprise decreased by 7.7% and 1.6%, the travel time of passengers decreased by 0.7% and 1.5%, respectively. Under the condition of meeting the demand of passenger flow, the optimized train operation plan can effectively reduce the operating cost of enterprises and save the travel time of passengers, which is conducive to the sustainable development of intercity railways.