Most of the urban rail transit enterprises in China have high construction and operation costs, while the government imposes price control on their fares, making their revenues unable to cover their costs and thus causing certain losses. In order to ensure the economic sustainability of urban rail transit enterprises, the government then subsidizes their losses. In the context of loss subsidies as the main subsidy mode for urban rail transit, the government regulates whether urban rail transit enterprises waste cost in order to protect social welfare and reduce the financial pressure of subsidies. This paper constructs an evolutionary game model between government regulators and urban rail transit enterprises, establishes replicated dynamic equations to obtain the evolutionary stabilization strategies of the government and urban rail transit enterprises under different situations, and analyzes the effects of various parameters on the cost control behaviors of urban rail transit enterprises under different loss-subsidy modes through numerical simulations. The theoretical study and simulation results show the following: When only the regulatory policy is adopted, the optimal strategy of urban rail transit enterprises may be cost saving or cost wasting under different subsidy models; if only the penalty policy is adopted, the enterprises will choose the cost wasting strategy when the penalty is small, and the enterprises will choose the cost saving strategy when the penalty is large; if only the fixed proportion subsidy model is adopted, no matter how large the proportion k of government subsidies is, the urban the optimal strategy for rail transit enterprises is cost wasting. If only the regressive loss subsidy model is adopted, the different sizes of its various parameter settings will also lead to the enterprises’ choice of cost wasting strategy or cost saving strategy. Therefore, the government should formulate corresponding policies according to different cost control objectives.