This study focuses on an environment-friendly toll design problem, where an acceptable road network performance is promised. First, a Traffic Performance Index (TPI)-based evaluation method is developed to help identify the optimal congestion level and the management target of a transportation system. Second, environment-oriented cordon- and link-based road toll design models are respectively proposed through the use of bi-level programming. Both upper-level submodel objectives are to minimize gross revenue (the total collected toll minus the emissions treatment cost) under different pricing strategies. Both lower-level submodels quantify the user equilibrium (UE) condition under elastic demand. Moreover, the TPI-related constraints for the management requirements of the network performance are incorporated into the bi-level programming modeling framework, which can lead to 0–1 mixed integer bi-level nonlinear programming for toll design problems. Accordingly, a genetic algorithm-based heuristic searching method is proposed for the two pricing models. The proposed cordon- and link-based pricing models were then applied to a real-world road network in Beijing, China. The effects of the toll schemes generated from the two models were compared in terms of emissions reduction and congestion mitigation. In this study, it was indicated that a higher total collected toll may lead to more emissions and related treatment costs. Tradeoffs existed between the toll scheme, emissions reduction, and congestion mitigation.