Based on the analysis of intercity travel links, this paper analyzes the influencing factors of passenger travel choice and introduces the psychological latent variables into the Logit model, and builds the SEMLogit model of passenger intercity travel choice based on travel chain. Through the investigation of the passenger flow in the ShanghaiHangzhou transport corridor, the application of the model and the parameter calibration are carried out, and the choice of intercity passenger travel chain is predicted with the relative error of less than 2%. The results show that the improved model that takes into account the psychological latent variables has a good explanatory power and can intuitively reflect and predict the traveler’s choice of travel modes in intercity travelling.