Integrated rice-frog farming (IRFF), as a mode of ecological farming, is fundamental in realizing sustainable development in agriculture. Yet its production of greenhouse gas (GHG) emissions remains unclear. Here, a randomized plot field experiment was performed to study the GHG emissions for various farming systems during the rice growing season. The farming systems included: conventional farming (CF), green integrated rice-frog farming (GIRF), and organic integrated rice-frog farming (OIRF). Results indicate that the cumulative methane (CH4) emissions from the whole growth period were divergent for the three farming systems, with OIRF having the highest value and CF having the lowest. For nitrous oxide (N2O) emissions, the order is reversed. IRFF significantly increased the dissolved oxygen (DO), soil redox potential (Eh), total organic carbon (TOC) content, and soil C:N ratio, which is closely related to GHG emissions in rice fields. Additionally, the average emissions of carbon dioxide (CO2) from soils during rice growing seasons ranged from 2312.27 to 2589.62 kg ha-1 and showed no significant difference in the three treatments. Rice yield in the GIRF and OIRF were lower (2.0% and 16.7%) than the control. The CH4 emissions contributed to 83.0-96.8% of global warming potential (GWP). Compared to CF, the treatment of GIRF and OIRF increased the GWP by 41.3% and 98.2% during the whole growing period of rice, respectively. IRFF significantly increased greenhouse gas intensity (GHGI, 0.79 kg CO2-eq ha-1 grain yield), by 91.1% over the control. Compared to the OIRF, GIRF decreased the GHGI by approximately 39.4% (0.59 kg CO2-eq ha-1 grain yield), which was 44.2% higher than that of the control. The results of structural equation model showed that the contribution of fertilization to CH4 emissions in paddy fields was much greater than that of frog activity. Moreover, frog activity could decrease GWP by reducing CH4 emissions from rice fields. And while GIRF showed a slight increase in GHG emissions, it could still be considered as a good strategy for providing an environmentally-friendly option in maintaining crop yield in paddy fields.