Nowadays, metro systems play an important role in meeting the urban transportation demand in large cities. The understanding of passenger route choice is critical for public transit management. The wide deployment of Automated Fare Collection(AFC) systems opens up a new opportunity. However, only each trips tap-in and tap-out timestamp and stations can be directly obtained from AFC system records; the train and route chosen by a passenger are unknown, which are necessary to solve our problem. While existing methods work well in some specific situations, they dont work for complicated situations. In this paper, we propose a solution that needs no additional equipment or human involvement than the AFC systems. We develop a probabilistic model that can estimate from empirical analysis how the passenger flows are dispatched to different routes and trains. We validate our approach using a large scale data set collected from the Shenzhen metro system. The measured results provide us with useful inputs when building the passenger path choice model.