Understanding the distribution of passenger flow is one of the crucial prerequisites for improving operational efficiency and implementing travel demand management strategies. This paper proposes an improved Random Regret Minimization (i-RRM) model based on the regret theory, where the passenger’s regret on selecting routes is minimized. Considering the growing trend of passengers relying on smartphone apps for route planning and navigation, three factors are investigated, namely, travel time, the number of transfer stations, and the total number of stations traveled. Automatic Fare Collection (AFC) is used to get the proportion of each route, and mobile phone signaling data is used to obtain the ground truth of passengers’ routes proportions for parameter calibration and model validation. The results show that, compared to the ground truth data, the average errors of the proposed i-RRM model, the classic RRM model, and the direct path matching algorithm are 6.03%, 8.96%, and 10.45%, respectively.