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Urban road traffic is one of the primary sources of carbon emissions. Previous studies have demonstrated the close relationship between traffic flow characteristics and carbon emissions (CO2). However, the impact of dynamic traffic distribution on carbon emissions is rarely empirically studied on the network level. To fill this gap, this study proposes a dynamic network carbon emissions estimation method. The network-level traffic emissions are estimated by combining macroscopic emission models and recent advances in dynamic network traffic flow modeling, namely, Macroscopic Fundamental Diagram. The impact of traffic distribution and the penetration of battery electric vehicles on total network emissions are further investigated using the Monte Carlo method. The results indicate the substantial effect of network traffic distribution on carbon emissions. Using the urban expressway network in Ningbo as an example, in the scenario of 100% internal combustion engine vehicles, increasing the standard deviation of link-level traffic density from 0 to 15 veh/km-ln can result in an 8.9% network capacity drop and a 15.5% reduction in network carbon emissions. This effect can be moderated as the penetration rate of battery electric vehicles increases. Based on the empirical and simulating evidence, different expressway pollution management strategies can be implemented, such as petrol vehicle restrictions, ramp metering, congestion pricing, and perimeter control strategies.