The station passing capacity is the key performance indicator to evaluate the planning and operation of railway stations. This paper mainly studies the calculation method about the effective passing capacity of railway stations that incorporates the train operation process into the calculation, which is of great significance for the theoretical research of station passing capacity calculation. At first, this paper introduces the concept of train operation chain, and then introduces the construction of double-layer alternative set based on train operation chains. On this basis, the effective passing capacity model of railway station is constructed. A case study based on the actual data of Jingping Logistics Park verifies the effectiveness of the model and the station technical operation scheduling is drawn based on the effective passing capacity. In the end, this paper analyzes the bottleneck of the logistics park's capacity and gives suggestions for capacity improvement.