The NH3, N2O and CO2 emissions from farmland soil pose a great threat to the environment, and the application of organic fertilizer and other reasonable fertilization measures can reduce soil gas emissions. However, research into greenhouse gas emissions and environmental benefits under the combined measures of partial substitution of organic fertilizer and phased application of chemical fertilizer is limited. Herein, a field experiment involving soil gas emission monitoring was conducted to study the effects of chemical fertilizer application in stages on Mollisols’ gas emissions and environmental benefits based on the partial replacement of chemical fertilizer with organic fertilizer. Five treatments were set up, including conventional nitrogen application (CF); no nitrogen application (N0); and one-stage (N1), two-stage (N2) and three-stage (N3) application of chemical nitrogen based on 25% of chemical nitrogen being replaced with organic fertilizer. The results showed that N1 had the best emission reduction. Compared with CF, N1 reduced NH3 volatilization and N2O and CO2 emission accumulation by 27.64%, 12.09% and 15.48%, respectively. Compared with N2 and N3, N1 could better reduce the soil urease, nitrate reductase, catalase and β-glucosidase activities, reduce the rate of the conversion of urea and organic carbon, increase the content of NH4+-N in the soil and reduce the NH3 volatilization rate and N2O and CO2 emission rates. A comprehensive analysis showed that N1 showed the best effects in reducing the soil gas emission rate, and environmental cost.