The combined application of organic and synthetic nitrogen (N) fertilizers is being widely recommended in China’s vegetable systems to reduce reliance on synthetic N fertilizer. However, the effect of substituting synthetic fertilizer with organic fertilizer on vegetable productivity (yield, N uptake and nitrogen use efficiency) and reactive nitrogen (Nr) losses (N2O emission, N leaching and NH3 volatilization) remains unclear. A meta-analysis was performed using peer-reviewed papers published from 2000 to 2019 to comprehensively assess the effects of combined application of organic and synthetic N fertilizers. The results indicate that overall, the vegetable yield, N2O emission and NH3 volatilization were not significantly changed, whereas N leaching was reduced by 44.6% and soil organic carbon (SOC) concentration increased by 12.5% compared to synthetic N fertilizer alone. Specifically, when synthetic N substitution rates (SRs) were ≤70%, vegetable yields and SOC concentration were increased by 5.5%–5.6% and 13.1–18.0%, and N leaching was reduced by 41.6%–48.1%. At the high substitution rate (SR>70%), vegetable yield was reduced by 13.6%, N2O emission was reduced by 14.3%, and SOC concentration increased by 16.4%. Mixed animal-plant sources of organic N preferentially increased vegetable yield and SOC concentration, and reduced N2O emission and N leaching compared with single sources of organic-N. Greenhouse gas (GHG) emission was decreased by 28.4%–34.9% by combined applications of organic and synthetic N sources, relative to synthetic N fertilizer alone. We conclude that appropriate rates (SR ≤ 70%) of combined applications of organic and synthetic N fertilizers could improve vegetable yields, decrease Nr and GHG emission, and facilitate sustainable development of coupled vegetable-livestock systems. Display omitted •Yields increased when substitution rate of synthetic N with organic source was ≤70%.•Substitution of synthetic N fertilizer with organic fertilizers reduced N leaching loss.•Substitution of synthetic N fertilizer with organic fertilizers increased soil carbon sequestration.•Combined applications of organic and synthetic N fertilizers decreased net GWP at field level. Capsule: Appropriate substitution of synthetic N fertilizer with organic fertilizers could increase vegetable yields and SOC concentration, and reduce N leaching and GHG emission.