With the increasing application of crop straw, the greenhouse gas emissions caused due to crop straw have received increasing attention. However, the current studies have not explored the greenhouse gas emissions from on-farmland consumption of returned straw. Based on a long-term positioning experiment, three treatments were set up in double-cropping rice fields: chemical fertilizer (CF), straw replacing 1/3 nitrogen fertilizer (MS), and straw replacing 2/3 nitrogen fertilizer (HS). We measured the biomass, soil properties, and greenhouse gas emissions of double-cropping rice and then comprehensively evaluated the global warming potential, carbon footprint, and net ecological and economic benefits. The straw treatments (MS and HS) increased the cumulative annual emissions of CH4 (98.44% and 261.23%), CO2 (30.85% and 122.29%), and N2O (7.37% and 52.50%), the cumulative annual global warming potential (74.15% and 206.12%), average GHG intensity (43.26% and 138.07%), and the annual cumulative net ecosystem carbon budget (52.96% and 100.97%) in the early and late rice growing seasons, respectively. We observed that the real-time greenhouse gas emissions were significantly correlated to the soil microbial functional genes and total carbon, NH4+-N, and NO3−-N. The results of the random forest model showed that total carbon (13.87%) and nirK abundance (9.80%) were the highest predictors of global warming potential at the booting and maturity stages, respectively during rice growing season. Combining the resource inputs for agricultural production and the greenhouse gas emission potential of the returned straw on its own, MS showed the lowest net greenhouse gas emission, and MS and HS showed significantly increased annual cumulative net ecological economic benefits (38.08% and 34.30%). Overall, MS showed the lowest net greenhouse gas emission and the highest net ecological economic benefits, which is a straw-returning measure with low environmental impact and high economic returns.