Air-rail intermodal freight transportation offers a promising solution to address the increasing demand for high-value and time-sensitive goods. In the transformation of transport mode, the connecting link was affected by the transport cost and transport efficiency of combined transport goods to a certain extent. Based on the external transfer connection mode of "all-cargo aircraft + high-speed rail freight train", a model was constructed for optimizing the connection timetable and ferry scheduling scheme in air-rail intermodal freight transportation to further optimize the air-rail intermodality scheme,. To solve this model, an approach based on genetic algorithms was developed. Connection cost and connection time were further analyzed. The model and approach were tested in a real-world case of air-rail freight transportation using the timetable data of Hongqiao Airport T2 Terminal and Shanghai Hongqiao High-speed Railway Station on a specific day. The simulation results show that three ferry cars are needed to transport the goods in the air-rail connection. In this scheme, the workload of each ferry car is reasonably distributed, and the cost of each batch of goods is the smallest. The connection cost accounts for about 20% of the total cost, and the cost advantage of air-rail intermodality in long-distance transportation is more obvious. The efficiency of loading and unloading is the key factor affecting the connection time of air-rail intermodality. It can provide a guidance for the future operation of long-distance air-rail intermodality.