<p>Organic fertilizer substitution for chemical fertilizer can reduce nitrogen(N) leaching, but the effect of different substitution ratios on N leaching is not clear. In this study, we conducted a meta-analysis with 421 observations from 44 peer-reviewed papers, to investigate the effects of climatic conditions, initial soil properties and management practices on N leaching from vegetable fields under different organic fertilizer substitution rates (SR), and quantified the contribution of each factor. The results indicated that compared with chemical fertilizer application, the N leaching of low (SR ≤ 35%), medium (35% &lt; SR ≤ 70%) and high (SR &gt; 70%) organic fertilizer substitution rate decreased by 24.8%, 53.7% and 55.3%, respectively. The highest yield increases of 13.2% under the three-SR was achieved with the medium SR. The random forest model explained 76.9% of the contribution of N leaching. Management practices exerted had the most significant effect on N leaching, with the effects of N application, irrigation and vegetable type ranking the top three among all the influences, reaching 35.6%, 29.4% and 22.8%, respectively. Among the soil properties contribution, soil texture had the largest influence factor of 20.4%. Whereas, among climatic factors, average annual temperature had the greatest influence of 15.2% on N leaching. A range of organic fertilizer SR between 35–70% was more conducive to increasing vegetable yields and maintaining soil N in Chinese vegetable systems.</p>