Municipal solid waste (MSW) is carbon-intensive and thus causes critical environmental and climate impacts. A material flow analysis has been carried out to compute carbon flows embodied in MSW across 31 provinces in Mainland China from 2000 to 2023, and greenhouse gases (GHGs) emissions of municipal waste estimated. By exploring changes in waste composition and spatio-temporal disparities in waste management, our emission estimation could be 15–40% smaller than conventional estimation employing a constant composition. Aggregately some 813 ± 179 megatonnes carbon (MtC) were contained in MSW in 2000–2023, creating net emissions equivalent to 2.37 ± 0.43 gigatonnes of CO2 (GtCO2e). MSW generation in China more than doubled during the period, net GHGs emissions increased by 1.8 times. The evolution of waste and carbon metabolism was driven by increment, composition, and management effects. Enhanced practices of waste management, particularly widespread promotion of waste sorting in cities as from 2019, have curbed GHGs emissions. GHGs intensity per tonne of MSW treatment had declined from 0.48 tCO2e in 2018 to 0.39 tCO2e in 2023. In the long run, the increment and composition effects may decline. Improved waste management integrating circular economy can minimize emissions and achieve a low-carbon transition for the municipal waste system.