Carbon and nitrogen are central elements in global biogeochemical cycles. To effectively manage carbon and nitrogen in China, we developed a comprehensive model for quantifying their fluxes, investigating their interplay across 16 human and natural subsystems. Between 1980 and 2020, nitrogen losses in China increased 2.3-fold and carbon emissions surged 6.5-fold. Integrated carbon and nitrogen management holds the potential for a 74% reduction in nitrogen losses to air and water and a 91% decrease in carbon emissions to the atmosphere by 2060. Compared with separate control of carbon or nitrogen, integrated management delivers an additional reduction of 1.8 million tons of nitrogen and 26.5 million tons of carbon by 2060, bringing out a 37% decrease in unit abatement cost and a net societal benefit of 1384 billion USD.