Green manures (GMs) are commonly used in reducing synthetic fertilizer input and mitigating environmental burden in paddy fields in China, but the contributions and comprehensive mechanisms of GMs are not illustrated clearly. We have established an experiment network of GM–rice rotation and have demonstrated extensively across eight provinces in southern China since 2008. Results from 201 site–year field experiments and the survey of GM's responses at 71 demonstration sites and 2062 farmers were collected. Compared with conventional synthetic N (CN) fertilization without GM, GM with 60% CN achieved the same level of rice yield, total amino acid concentration increased by 62.64% in the grains, and CN use efficiency increased by 15.8%, whereas the C footprint, reactive N loss, and N footprint decreased by 30.81%, 19.18%, and 9.65%, respectively. This quantitative analysis of green manuring provides support to rice production with low N input in southern China.