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Manure replacing synthetic fertilizer is a viable practice to ensure crop yield and increase soil organic carbon (SOC), but its impact on greenhouse gas (GHG) emissions is inconsistent, thus remains its effect on CF unclear. In this study, a 7-year field experiment was conducted to assess the impact of replacing synthetic fertilizer with manure on crop productivity, SOC sequestration, GHG emissions and crop CF under winter wheat–summer maize cropping system. Five treatments were involved: synthetic nitrogen, phosphorus, and potassium fertilizer (NPK) and 25%, 50%, 75%, and 100% of manure replacing synthetic N (25%M, 50%M, 75%M, and 100%M). Compared with NPK treatment, 25%M and 50%M treatments maintained annual yield (winter wheat plus summer maize) and sustainable yield index (SYI), but 75%M and 100%M treatments significantly decreased annual yield, and 100%M treatment also significantly reduced annual SYI. The SOC content exhibited a significant increasing trend over years in all treatments. After 7 years, SOC storage in manure treatments increased by 3.06–11.82 Mg ha−1 relative to NPK treatment. Manure treatments reduced annual GHG emissions by 14%–60% over NPK treatment. The CF of the cropping system ranged from 0.16 to 0.39 kg CO 2 eq kg−1 of grain without considering SOC sequestration, in which the CF of manure treatments lowered by 18%–58% relative to NPK treatment. When SOC sequestration was involved in, the CF varied from −0.39 to 0.37 kg CO 2 eq kg−1 of grain, manure treatments significantly reduced the CF by 22%–208% over NPK treatment. It was concluded that replacing 50% of synthetic fertilizer with manure was a sound option for achieving high crop yield and SYI but low CF under the tested cropping system. • Manure replacing ≤50% fertilizer maintained annul crop yield and its sustainability. • Manure substitution increased the soil organic carbon storage. • Manure substitution reduced greenhouse gases emissions. • Manure substitution reduced the crop carbon footprint due to the soil organic carbon increase. [ABSTRACT FROM AUTHOR]