The carbon emission boundaries of the gray rainwater drainage system of residential and commercial areas of Nanjing, a typical city in the Yangtze River Delta were defined, and a combination of field monitoring and numerical simulation was employed to quantify the operational phase carbon emissions. The influence of factors such as functional zone type, drainage mode, and storage mode on operational carbon emissions under different rainfall return periods was investigated. Additionally, the proportion of operational phase emissions in the full life cycle was calculated. The results indicate that carbon emissions from initial rainfall runoff are the primary source of operational phase carbon emissions in gray rainwater drainage systems. The average carbon emission from initial runoff in commercial areas was 3.76 t/hm²(in CO2 equivalent), 1.95 times that of residential areas (1.93 t/hm2). Under forced drainage mode, operational phase carbon emissions were 2.273.47 times higher than those under gravity drainage mode, while storage mode reduced operational phase carbon emissions by 28.76% by controlling initial rainfall runoff. Across the full life cycle of gray rainwater drainage systems, operational phase carbon emissions accounted for 15.98%31.87%, depending on functional zone type, drainage mode, and storage mode.