Lateral runways have gradually popularized in the planning and design of large airports in China because they can flexibly face the influence of strong crosswind and thus improve the efficiency of airports. However, few studies on lateral runways have emerged globally, and research on runway capacity model of lateral runways is of great significance. In this paper, the wake effect between aircraft on a set of lateral runways is considered for the system with two lateral runways. The release conditions of aircraft on the lateral runways are given by calculating the wake dissipation time. At the same time, the conditions for inserting departing aircraft between continuously approaching aircraft in the system with two lateral runways are obtained by using the timing chart. Thus, the runway capacity calculation model of the system with two lateral runways is constructed. Finally, Chengdu Tianfu International Airport Phase I runway is taken as an example to calculate the hourly capacity of each runway under the influence of wake flow, and a flight take-off and landing schedule is given to verify the correctness of the model, which provides a reference for the theoretical calculation model of runway capacity for lateral runway airports.