Here, we report on a three-year field experiment that used an integrated soil - crop system management (ISSM) approach, to improve crop (pepper) yield and to cut carbon (C) and nitrogen (N) footprints of greenhouse vegetable production in the Yangtze River Basin, China.Treatments included farmers practice for nutrient inputs, soil and crop management; soil remediation, soil management, including control of soil borne pathogens and reduced nutrient input by organic resources; and ISSM, which includes combined optimization of factors, including soil remediation, reduced planting d., and improved timing of inorganic fertilizer applications.Measurements of pepper yield and N concns, N offtake, and C and N footprints were calculated using life cycle assessment.Reactive nitrogen (Nr) losses from FP, SR, and ISSM treatments were 82, 52 and 59 kg N ha-1, resp.Greenhouse gas emissions of FP, SR, and ISSM treatments were 7061, 5279 and 5728 kg CO2-equiv ha-1, resp.N and C footprints of the ISSM treatment were significantly lower than the FP treatment by 39% and 30%, resp., as a result of both a 46% reduction in N inputs (especially an 80% reduction in organic N inputs) and a greater yield.Yield increase contributed to 26% and 37% the reduction of N and C footprints in ISSM treatment, resp.ISSM strategy can produce greater pepper yields with lower environmental costs, and can contribute to sustainable greenhouse vegetable production, and that SR, while being single factor strategy, is a useful first step towards ISSM.