A key strategy of sustainable transportation, parking pricing can directly contribute to decreased greenhouse gas emissions and air pollution. This paper describes an optimal structure of parking rates in terms of parking locations and time of day. A two-level parking model based on game theory is established using parking survey data collected in Beijing in 2014. The model was estimated based on Stackelberg game and the Nash equilibrium. Using the two-level parking model, the optimal structure of parking rates for inside/outside business zones and during peak/off-peak hours was calculated. In addition, the relationship between the government (which represents the public benefit) and car users, as well as the relationships among car users in the parking system were investigated. The results indicate that equilibrium among all of the agents in the parking system can be obtained using the proposed parking rate structure. The findings provide a better understanding of parking behavior, and the two-level parking model presented in the paper can be used to determine the optimal parking rate to balance the temporal and spatial distribution of parking demand in urban areas. This research helps reduce car use and the parking-related cruising time and thus contributes to the reduction of carbon emissions and air pollution.