Manure application is an important approach for improving soil fertility and grain production. The effectiveness of the nutrients in manure is affected by many factors, such as climatic conditions and soil properties, which may lead to different contributions of manure to crop yield. This study was carried out to explore the increment in grain yield with manure application in different climatic regions and soil types for understanding the effect of manure application on crop yield at national and regional levels in China. The results can be helpful for developing manure management strategies. This study was conducted using 402 grain yield datasets collected from 109 published articles regarding three major food crops, namely wheat, maize, and rice. The treatments tested were no fertilization(CK);chemical N, P, and K fertilization(NPK); and NPK fertilization combined with manure application(NPKM). Differences in yield among the application of CK, NPK, and NPKM in the three crops across four regions of China were studied using meta-analysis. The importance of climatic parameters and soil properties on positive manure effects was quantified using random forest analysis. Compared with NPK, NPKM treatment resulted in increments of 5.6%, 7.6%, and 4.5% in grain yield for wheat, maize, and rice, respectively, with an average increase of 4.7% across the three crops. The yield increment by manure application varied across regions as follows:northwestern China > northeast and north China > southern China > eastern China. The highest yield enhancement by manure application was observed in the temperate continental climate zone, followed by the temperate monsoon and subtropical monsoon climate zones. Average annual rainfall was the main factor that affected the yield response to manure for wheat and rice, while the main factors affecting the yield response of maize were the mean annual temperature and frost-free period. The yield increment by manure application was higher in soils with lower soil organic matter(SOM)and total nitrogen(TN)content than those with higher SOM and TN content, suggesting that SOM and TN are essential factors that influence the ability of manure to improve grain production among the analyzed soil properties. Nationally, manure application can significantly increase crop yields, especially in areas with insufficient soil nutrients, low temperature, and low rainfall.