The integrated urban drainage system has complicated sources of greenhouse gases (GHG) emissions, which is one of contribute to climate change. As a new model of low-carbon ecological city development in China, sponge city has great potential of carbon emission reduction. However, limited by the lack of awareness of the importance of carbon emissions from integrated urban drainage system, few studies have focused on the impact of sponge city construction on the carbon emissions from integrated urban drainage system. This study proposed an accounting framework for carbon emissions from integrated urban drainage system. The emission factor method was used to calculate carbon emissions. A case study was conducted in Xiamen, China, the carbon emission level of integrated urban drainage system and the carbon emission reduction effect of sponge city construction were discussed. The results show that the carbon emission from traditional city drainage system and sponge city drainage system accounts for about 3.4% and 1.7% of the city's carbon emission, respectively. Wastewater treatment and Sludge Treatment and Disposal are the main contributors to the carbon emissions from integrated urban drainage system. Electricity consumption is the main contributors to the indirect carbon emissions. Adjusting the sludge disposal method has the best carbon emission reduction effect, raising the standard of wastewater treatment plant tail water will lead to an increase in carbon emissions. Compared with the traditional city drainage system, the sponge city drainage system can reduce carbon emissions from integrated urban drainage system by an average of 49%, and the corresponding economic benefit was approximately 91–297 CNY/104 m3 wastewater. This study plays a positive role in understanding the carbon emission level of integrated urban drainage system and planning the low-carbon development of the city in the future.