Globally, paddy fields are a major anthropogenic source of greenhouse gas (GHG) emissions from agriculture. There is, however, limited understanding of relationships between GHG production with fertilizer management, rice varieties, and soil variables. This information is crucial for minimizing the climatic impacts of rice agriculture. Here, we examined the relationships between soil GHG production and management practices throughout China. The current doses of N-fertilizer (73-272 kg ha−1) were negatively correlated with rice yield and with CO2 or CH4 production and positively correlated with N2O production, thus suggesting N-overfertilization. Impacts on soil traits such as decreasing pH or the availabilities of other nutrients could be underlying these relationships. Rice yield was highest, and GHG production was lowest at sites using intermediate levels of P- and K-fertilization. CO2 and CH4 production and emissions were positively related with soil water content. The yield was higher, and N2O productions were lower at the sites with japonica rice. Our results strongly suggest that current high doses of N-fertilizers could be reduced to thus avoid the negative effects of excessive N input on GHG production without any immediate risk of rice production loss. Current intermediate doses of P- and K-fertilization should be adopted across China to further improve rice production without the risk of GHG emissions. The use of different rice varieties and strategies of water management should be reexamined in relation to crop production and GHG mitigation.