In recent years, transportation problems have evolved from city transportation problems to urban agglomeration problems. Thus, the development of Chinese transportation cannot neglect the role of Inter-City transportation being the infrastructural framework. Keep abreast of Inter-City passengers’ choice behaviors can support the operation of multi-transportation systems. First, to better address the large deviation between the impedance function and the travelers’ perceived cost, we construct the generalized cost function with seven terms, which are car time, waiting time, walking time, access/egress times, ticket price, transfer penalty and comfort level respectively, with reliability and security being taken into considerations. Second, pointing at the problem of low accuracy in calculating the sharing rate of various transportation modes under different traffic systems, we proposed a Two-Stage Path-Size Weibit (TS-PSW) model to calculate the sharing rate of multi-mode passenger flow between cities respectively. After that, we decomposed the TS-PSW model into two-layer Path-Size Weibit (PSW) model by the Two-Stage estimation method, and used the maximum likelihood estimation to solve PSW model respectively. Finally, using the intercity transportation networks (Chengdu–Chongqing, Guangzhou–Qingyuan, Beijing–Zhangjiakou) as background, compare six discrete choice models’ calculation results. Result shows that the passenger flow sharing rate curve calculated by TS-PSW Model is evidently the closest to the actual transportation modes, the maximum error from Chengdu to Chongqing is 6.60%, the minimum is 3.80%, the maximum error from Beijing to Zhangjiakou is 10.20%, and the minimum is 3.30%. Results verify the effectiveness of the proposed generalized cost function and mode choice model. The upcoming Winter Olympics will be held during the Spring Festival, other events will not be arranged at the same time. Therefore, travel demand will increase significantly. Improving the mode choice model and verifying its effectiveness on multiple intercity networks, especially the Beijing–Zhangjiakou network, can provide theoretical support for mastering passenger travel mode selection during the future Winter Olympics and further improving transportation planning and related deployment.