To meet the demand of direct passenger travel within the scope of urban agglomeration, the through lines plans based on the connection of multi-level rail transit were proposed, and the gain effects of passenger transport system brought by different plans were discussed. The specific contents are as follows:a super network model of urban agglomerations multi-mode transportation was constructed based on the theory of hyper network. The generalized travel cost of passenger super path was quantified. A bi-level programming model for the optimal setting of through lines was constructed, in which the upper level programming considered the profit of the transporter and the saving of the passenger travel cost brought by the setting of through lines. The lower level programming was a balanced allocation model for the multi-mode transportation system of urban agglomeration. Genetic algorithm and successive average method were used to solve the upper and lower level models. Finally, the passenger lines connecting the main hubs in Beijing-Tianjin-Hebei Urban Agglomeration were taken as an example to illustrate the performance and applications of the model, and the rationality of the scale of the through line was demonstrated. The results show that, there are 11 alternatives through lines between Beijing Capital International Airport, Beijing railway station, Beijing West Railway Station, Beijing South Railway Station and Tianjin railway station. The best through lines are No. 1, 2, 5, 6, 7and 9. The reasonable scale of the direct line is 3 at present. After opening, the system benefit will increase by 28.03% and the average travel time of passengers will reduce by 10.02%. © 2024 Editorial Board of Jilin University. All rights reserved.