In this paper, the common line problem and passengers’ choice behaviors in transit networks are revisited and discussed. The concept of the common line problem is extended to represent a common route problem in transit networks. The transit routes are classified into various levels of attractive route sets according to route fixed costs and route frequencies. The transit passenger assignment problem on congested transit networks is defined to assign passenger flows on attractive route sets and is formulated as a variational inequality (VI) problem. In the proposed model, the effective frequency approach is applied to reflect the effects of passenger congestion on the waiting time at the stations. Compared with traditional models, the proposed passenger flow assignment model does not require a modification to the transit network nor a constant recomputation of the changing attractive line set. Finally, a simple example is used to illustrate the difference between common line and common route methods, and the passengers’ travel behaviors under various transit conditions are demonstrated on the Sioux Falls transit network.