Aims We studied the effects of green manuring on the nitrogen (N) cycling process in different paddy soils.Methods Field experiments conducted in Hunan, Jiangxi, Henan and Fujian provinces in south China to investigate the responses of rice yield, soil properties, and functional genes involved in N cycling to green manuring. The field experiments had four treatments, i.e., no fertilizer application (NF), using milk vetch (Astragalus sinicus L.) as green manure without chemical fertilizer (GM), winter fallow and chemical fertilizer (CF), and a combination of green manure and chemical fertilizer (GMCF). Results The results showed that rice yield significantly increased in GMCF treatment. The copies of nifH gene significantly increased in GMCF in Jiangxi and Henan provinces. Ammonia oxidizing archaeal (AOA) amoA gene was predominant in all provinces compared with ammonia oxidizing bacterial (AOB). Compared with CF treatment, The copies of AOB-amoA gene were reduced in GMCF, indicating the inhibition of soil nitrification. The nirK gene was negatively correlated with SOM, TN, NH4+-N, NO3--N and AP, indicating that the positive effects of green manure on soil nutrients caused the inhibition of denitrification process. The nirK gene was the most critical factor influencing rice yield among the tested functional genes, with a relative influence of 63.5%. In comparison SOM was the most important factor (with a relative influence of 41.0%) among soil chemical properties. Conclusions In conclusion, the application of green manures changed the abundance of functional genes involved in the N cycling, and combined application with chemical fertilizer inhibited soil nitrification and denitrification.