The study on carbon emissions of urban wastewater treatment system based on the “water-energy-carbon” nexus can reveal the internal relationship between resource flow, input process, and carbon emissions of a wastewater treatment system, and can provide important references for low-carbon operation and management of wastewater treatment systems. Based on the “water-energy-carbon” nexus, a theoretical framework and accounting method of carbon emissions of urban wastewater treatment system are constructed. The wastewater treatment plant (WWTP) in Zhengzhou City was taken as a case study. Carbon emissions of different links in the operation of the wastewater treatment system were evaluated. Analysis was also made on the factors that affect the dynamic change of carbon emissions in each link of the wastewater treatment system. The research results show that: (1) Among the carbon emissions generated by the operation of the wastewater treatment system, direct carbon emissions are dominant, and indirect carbon emissions (carbon emissions of energy consumption and carbon emissions of material consumption) are relatively small. (2) CH₄ and N₂O emissions per unit volume of wastewater treatment are mainly affected by wastewater treatment volume and water quality. (3) Carbon emissions of energy consumption and material consumption per unit volume of wastewater treatment decrease with the increase of the wastewater treatment volume. (4) Carbon emissions of urban wastewater treatment system are impacted by many factors, such as, wastewater treatment process, wastewater treatment capacity, operating conditions, post-treatment water quality requirements, treatment rate of returned water, and energy consumption types. It is of great significance for the low carbon operation of wastewater treatment system to strengthen the comprehensive management of resource input and circulation process of urban wastewater treatment system, and to promote synergy between water, energy saving, and carbon emissions reduction.