Passenger choice behavior, which causes dynamic changes of the passenger flow distribution and leads to the spread of congestion, is one of the key factors of bottleneck for passenger transport capacity. An association network of facilities is set up based on the analysis of passenger service chain in station. Then the passenger flow distribution model with node capacity constraints is established considering the passenger choice behavior. The dynamic penalty function is introduced to solve this model. Based on the result of the solution, the identification of bottleneck for passenger transport capacity through the index of affected degree of nodes is proposed. Finally, a case study of Lujiabang Road Station in Shanghai is carried out and compared with the simulation results of StaPass, verifying the feasibility and accuracy of this approach, which can help to analyze the passenger flow distribution of metro station in different scenarios.