Peatlands store large amounts of carbon in wetland ecosystems. The hydrological conditions within peatlands are important factors that affect the biochemical cycle and patterns of greenhouse gas emissions in these peatlands. This study was carried out in Changbai Mountain Jinchuan peatland to investigate variations in carbon dioxide and methane emissions in peat swamps that have undergone distinct saturation conditions. Three peatland types (high water levels (S1); medium water levels (S2); low water levels (S3)) at different flood depths were selected as specific sampling points. The static box and gas chromatography methods were used at different time periods (6:00; 12:00; and 18:00) from July to September. The discharge flux of CO2 and CH4 slowly increased with the increase in the water level. The results indicate similarity in the fluctuation trends between the fluxes of CO2 and CH4 in S1 and S2 to the fluctuations of water levels. During the entire growth season, the flux range of CO2 and CH4 was −695.329~859.907 mg m2h−1 and 259.981~147.155 mg m2h−1, respectively. Furthermore, there was variation in mutation characteristics between two gases, the CO2 exhibited larger mutation range (−7.08~3.40) than CH4 (−1.79~1.26). In terms of daily flux changes, CO2 showed an upward trend, while CH4 had a downward trend. These results indicate variations in saturation conditions tend to affect discharge of greenhouse gases, with subsequent effects on climate change. This study highlights potential theoretical support to reduce anthropogenic activities on peatlands. This can be achieved by undertaking measures to conserve peatlands and explore mitigation measures to minimize greenhouse gas emissions and hence impacts of climate change.