To analyze the law of passenger transportation economic policy in different operators, based on game theory to describe the Nash equilibrium among urban passenger transportation operators, a bi-level programming model is proposed to model urban passenger transportation operators’ economic decision-making, operators’ profit and social cost have been discussed, including the travel time cost, air pollution cost and energy consumption cost. The upper-level model describes the management authority’ regulation on the fares of each mode, the lower-level model describes the operators’ maximum profit by determining the service frequency. Based on GAMS and genetic algorithm, a numerical example verifies the validity of the proposed model. The introduction of subway service will increase the total market share of passenger public transportation, and effectively reduce the external cost, including the environmental emission cost and energy consumption cost.