Reducing the emissions of greenhouse gases (GHG) from paddy fields is crucial both for the sustainability of rice production and mitigation of global climatic warming. The effects of applying industrial and agricultural wastes as fertilizer on the reduction of GHG emissions in cropland areas, however, remain poorly known. We studied the effects of the application of 8 Mg ha−1 of diverse wastes on GHG emission and rice yield in a subtropical paddy in southeastern China. Plots fertilized with steel slag, biochar, shell slag, gypsum slag and silicate and calcium fertilizer had lower total global-warming potentials (GWP, including CO2, CH4 and N2O emissions) per unit area than control plots without waste application despite non-significant differences among these treatments. Structural equation models showed that the effects of these fertilization treatments on gas emissions were partially due to their effects on soil variables, such as soil water content or soil salinity. Steel slag, biochar and shell slag increased rice yield by 7.1%, 15.5% and 6.5%, respectively. The biochar amendment had a 40% lower GWP by Mg−1 yield production, relative to the control. These results thus encourage further studies of the suitability of the use waste materials as fertilizers in other different types of paddy field as a way to mitigate GHG emissions and increase crop yield.