Organic fertilizer is an effective substitute for mineral fertilizer that improves crop yield and is environmentally friendly. However, the effects of substitution often vary due to complicated interactions among the organic fertilizer substitution rate (Rs), total nutrient supply, and type of cropping system used. We performed a meta-analysis of 133 maize studies, conducted worldwide, to assess maize yield and environmental performance with substitution of mineral fertilizer with organic fertilizer. At an equivalent nitrogen (N) rate, substituting mineral fertilizer with organic fertilizer increased maize yield by 4.22%, reduced NH3 volatilization by 64.8%, reduced N leaching and runoff by 26.9%, and increased CO2 emissions by 26.8%; however, it had no significant effect on N2O or CH4 emissions. Moreover, substitution with organic fertilizer increased the soil organic carbon sequestration rate by 925 kg C ha−1 yr−1 and decreased the global warming potential by 116 kg CO2 eq ha−1 compared with mineral fertilizer treatment. The net global warming potential after organic fertilizer substitution was −3507 kg CO2 eq ha−1, indicating a net carbon sink. Furthermore, the effect of organic fertilizer substitution varied with the fertilization rate, Rs, and treatment duration. Maize yield and nitrogen use efficiency tended to increase with increasing N application rate following substitution of mineral fertilizer with organic fertilizer. Full substitution reduced N losses more than partial substitution. Further analysis revealed that the yield-optimal Rs for organic N in maize production was 40–60%. Moreover, maize yield and nitrogen use efficiency were further increased after long-term (≥ 3 years) combined use of organic and mineral fertilizers. These findings suggest that rational use of organic and mineral fertilizers improves maize productivity, increases soil organic carbon sequestration, and reduces N and C losses.