In order to overcome the difficulty in estimating the indirect carbon emissions from new energy vehicles due to the energy consumption in a large-scale expressway network, this paper proposes a new carbon emission calculation method of new energy vehicles based on the toll data in expressway ETC network. Firstly, the traffic flow data of new energy vehicles on expressways were cleansed and processed. Then, according to the distribution of toll gantries, road sections were defined and segmented. On this basis, the energy consumption of different types of new energy vehicles was analyzed. Furthermore, a carbon emission quantification model of new energy vehicles in the operational stage was established. Finally, by taking Guangdong Province as an example, the carbon emissions of new energy vehicles on expressways were calculated, with its spatial distribution characteristics being also analyzed. The results show that (1) Category 1 pure electric passenger cars are the main source of carbon emissions from new energy vehicles on expressways, accounting for 74.20% of the total carbon emissions of new energy vehicles, followed by Category 1 pure electric trucks, whose carbon emissions account for 14.18% of the total, and Category 1 plug-in hybrid passenger cars contribute 11.62% of the total; (2) the cities in the Pearl River Delta urban agglomeration are the main contributors to high carbon emissions from new energy vehicles, and the less developed regions in eastern, western and northern Guangdong account for less than 13% of the total carbon emissions from new energy vehicles; (3) the road segments with high carbon emissions from new energy vehicles mainly locate in the transportation hubs and inner-city expressway rings of developed cities, and Guangzhou metropolitan area as well as Shenzhen metropolitan area as the center has a radiating effect on the expressway network of surrounding cities; and (4) in less developed areas, due to the low density of expressway network and relatively lagging infrastructure, the penetration rate of new energy vehicles is low, the corresponding carbon emissions from new energy vehicles are generally low.