Application of biochar to rice has shown to elicit positive environmental and agricultural impacts due to its physicochemical properties. However, the relationship between greenhouse gas (GHG) emissions, rice yield, and soil nutrient status under biochar amendment remains unclear. In this study, rice yield and methane (CH4) and nitrous oxide (N2O) emissions were quantified in response to biochar application rate (0, 10, 20, and 40 t ha−1) to early and late subtropical rice cropping systems. We found that application of 10 t of biochar ha−1 to early rice reduced average CH4 emission fluxes, while all biochar application rates diminished average emissions in late rice paddy. Total global warming potential (GWP) and GHG intensity (GHGI) were inherently greater in late rice than early rice cropping. In early rice, GWP and GHGI were found to be similar between soil control, 10 and 20 t of biochar ha−1 treatments, although the largest occurred in the 40 t of biochar ha−1 treatment, whereas in late rice cropping, they were not affected by biochar application rates. Compared to the nil-biochar application, biochar application at varied rates did not affect rice yield. However, compared to 10 t biochar ha−1, increasing biochar application rate to 40 t ha−1 significantly decreased total rice yield (sum of early and late cropping). Generally, application of biochar increased soil salinity and total Fe and Fe2+ content while reducing soil bulk density. Temporal effects of biochar application were noted on CH4 emission flux, soil temperature, and soil Fe2+ and Fe3+ in early rice; and soil temperature, salinity, NH4+-N, NO3−-N, and soil Fe2+ and Fe3+ in late rice. This study confirms that the application of biochar at the lower rate of 10 t ha−1 is optimal for maintaining rice yield while reducing GHG emissions. Moreover, the study demonstrates the potential benefit of biochar in sustainable subtropical rice production.