In this paper, we propose a model-based perimeter gating control approach to improve network-wide emissions in an urban traffic network. An accumulation-based Macroscopic Fundamental Diagram (MFD) model of a single reservoir city is developed to describe the evaluation of traffic flows in a network. Moreover, a path flow distribution scheme using Dynamic User Equilibrium (DUE) discipline is designed to reproduce driver's adaptation to controlled flow. Perimeter gating control scheme using the Nonlinear Model Predictive Controller (NMPC) is developed to track the optimal green routing coefficient which will indirectly track the network-wide emission levels by manipulating the traffic flows into a reservoir. Simulation results show the effectiveness of the proposed scheme in improving the traffic emissions inside and outside the perimeter. Comparative analysis of nocontrol and NMPC shows that the proposed NMPC-based network-wide emission control strategy outperforms.