SUMMARYRice (Oryza sativaL.), wheat (Triticum aestivumL.) and maize (Zea maysL.) are the main crops grown in China. Applying organic manures is an important practice in sustaining soil fertility and agricultural productivity in these cropping systems. The current paper presents the effects of manure application on grain yields in nine long-term experiments that consist of one continuous maize, four wheat–maize and four rice-based cropping systems across a wide range of agro-ecological regions in China. The study shows that regular manure application can increase soil organic carbon (SOC) and grain yield across all the sites. Overall, regular use of manure results in larger increases in SOC in the maize and wheat–maize systems than in the rice-based systems. Application of manure tends to increase the grain yield in the maize and wheat–maize systems during the final years, but increases the grain yield in the rice-based systems during the initial years of the long-term experiments. There is only one site that shows significant improvement in the yield trend in association with the application of manure. The effects of manure on yield trends are probably determined by the initial yield and/or the ‘organic C effect’ that may cause gradual improvements in SOC and soil physical properties.