Based on the framework of method of successive averages(MSA), a modified stochastic user-equilibrium assignment algorithm was proposed, which can be used to calculate the passenger flow distribution of urban rail transit(URT) under network operation. In order to describe the congestion's impact to passengers' route choices, a generalized cost function with in-vehicle congestion was set up. Building on the k-th shortest path algorithm, a method for generating choice set with time constraint was embedded, considering the characteristics of network operation. A simple but efficient route choice model, which was derived from travel surveys for URT passengers in China, was introduced to perform the stochastic network loading at each iteration in the algorithm. Initial tests on the URT network in Shanghai City show that the methodology, with rational calculation time, promises to compute more precisely the passenger flow distribution of URT under network operation, compared with those practical algorithms used in today's China.
