To accurately describe features of passengers’ route choice behaviors of feeder bus lines, this research took the commuting trips during morning peak period under a typical commuting OD as study object, and established a passenger flow assignment model based on Logit-SUE model, which considers the relationship between the actual arrival time of passengers and the arrival time of vehicles. This model proposed a detailed quantitative description of the passengers’ queuing process at bus stations and improved the existing calculation method of waiting time at bus stations in the generalized travel cost measuring. Then the feasibility of the model was verified by comparison with previous studies, and the influences of the time step length t- and passengers’ perception coefficient of the path cost θ on the choice probabilities of different bus lines were analyzed. Results indicated that the modelling results will not have a big change when t- changes. Smaller t- leads to more accurate calculation results of waiting time. If all the commuters start at time t-, the model results in this paper correspond with that of the previous studies. However, when θ is small, there is a certain gap between the passenger perceived route costs and the actual costs. Big θ makes passengers feel closer to the reality of impedance so when θ is bigger, the choice probabilities of feeder bus lines with low costs are bigger.