This study was set to explore the response of CO2 and CH4 emission fluxes and its environmental factors (temperature and moisture) to green manure incorporation on typical yellow soil and limestone soil in Guizhou Province. We used a pot experiment with five treatments, including control(no green manure), Vicia villosa, Medicago sativa, Lolium perenne and Brassica napus. The results showed that green manure treatments increased soil CO2 emission compared with the control treatment, and the average CO2 flux and cumulative CO2 emission were higher in yellow soil than those in limestone soil. While the average CH4 flux and cumulative CH4 emission were higher in limestone soil than those in yellow soil. Green manure treatments increased global warming potential(GWP). Lolium perenne treatment had the highest GWP in both yellow soil and limestone soil, followed by Brassica napus green manure treatment, indicating that the contribution of non-legume green manure to soil GWP was greater than that of legume green manure. Soil type, green manure and their interactions had significant effects on CO2 emission flux, and soil CO2 emission was mainly driven by soil moisture, while CH4 emission flux was only affected by soil type. Visibility, green manure incorporation in yellow soil and limestone soil could increase CO2 emission, which had a positive effect on improving soil fertility and productivity.