To reduce reliance on synthetic nitrogen (N) fertilizer and sustain food production, replacing synthetic N fertilizer with animal manure as an effective method is widely used. However, the effects of replacing synthetic N fertilizer with animal manure on crop yield and nitrogen use efficiency (NUE) remain uncertain under varying fertilization management practices, climate conditions, and soil properties. Here, we performed a meta-analysis of wheat (Triticum aestivumL.), maize (Zea maysL.), and rice (Oryza sativaL.) based on 118 published studies conducted in China. Overall, the results indicated that substituting synthetic N fertilizer with manure increased yield by 3.3%−3.9% for the three grain crops and increased NUE by 6.3%−10.0%. Crop yields and NUE did not significantly increase at a low N application rate (≤120 kg ha−1) or high substitution rate (>60%). Yields and NUE values had higher increases for upland crops (wheat and maize) in temperate monsoon climate/temperate continental climate regions with less average annual rainfall (AAR) and lower mean annual temperature (MAT), while rice had higher increases in subtropical monsoon climate regions with more AAR and higher MAT. The effect of manure substitution was better in soil with low organic matter and available phosphorus. Our study shows that the optimal substitution rate was 44% and the total N fertilizer input cannot be less than 161 kg ha−1when substituting synthetic N fertilizer with manure. Moreover, site‐specific conditions should also be considered.