Literature review indicates that little is known about traveler behavior, such as transfer and route choices, in large transit systems because of the number of alternative routes involved and lack of empirical data. Even though many transit route assignment models have been developed and ample automated fare collection data have been collected, nearly no study has quantified how accurate resulting flow assignments are, especially for transfer flows. However, as a multi-stakeholder system, it is essential to estimate passenger flows over the Beijing rail transit network for revenue sharing and daily management/operation purpose. In this paper, major factors (including total travel time and transfer cost) that influence passenger flow pattern in the Beijing rail transit network are considered in a logit-based network flow assignment model. Specifically, a full transfer cost function, including transfer walking time, vehicle waiting time, and a penalty to additional transfers, is proposed to better simulate passengers' transfer behaviors. A generalized cost function for urban rail transit network is presented, and the corresponding route choice behavior of travelers is analyzed. An improved logit-based model is then presented for solving this network flow assignment problem. The depth-first method is used to search for "effective paths" among all O-D pairs. The average errors of estimated transfer flows from the proposed assignment model, which is proven to be more realistic in searching a set of effective paths, are below 20%. The results indicate that the models being developed in this study are capable of reasonably reproducing passengers' transfer and route choices and thus helpful for understanding the transfer behaviors of passengers of large rail transit networks. Copyright the fare of operational lines, except for the airport line, was adjusted to ¥2 (about $US0.3) only, and transferring between these lines does not require any additional charge.As BRTN is expanding quickly, the challenge is to predict the growth of travel demand and understand passengers' behaviors, such as line, route, and transfer location choice, and adjust the operation and management of the system accordingly. In addition, the construction of BRTN has been funded by multi-stakeholders besides the government, and there is a need to share the revenue on the basis of certain statistics, such as the travel demand served by a particular line. For example, the operator of metro line #4 is the Beijing MTR Corporation, which is financed by the Beijing Infrastructure Investment Corporation, the Beijing Capital Group, and the MTR Corporation (Hong Kong), whereas the operator of the other lines is the state-owned Beijing Subway Co., Ltd. This multi-stakeholder status makes it a necessary and critical task to scientifically predict passenger flow distribution within the BRTN for effective operation, management, and revenue allocation.An automatic fare collection (AFC) system was in effect for BRTN since June 2008. Through the AFC system, the O-D i...