Abstract: Global warming and eutrophication have become the dual pressures faced by lake ecosystems in recent years. They can affect greenhouse gas emissions and carbon cycling processes by altering water temperature and nutrient concentrations. However, the mechanism by which warming and eutrophication interact to affect CO₂ and CH₄ emissions remains unclear. This study conducted a mesocosm simulation experiment at the National Field Science Observation and Research Station of the Xingkai Lake Wetland Ecosystem in Heilongjiang from August to October 2024. The experiment simulated the climate change and eutrophication trends of the mid-21st century, aiming to investigate the characteristics and response mechanisms of CO₂ and CH₄ fluxes at the water-air interface of shallow lakes under different warming and nutrient conditions. The results indicated that in all groups, dissolved oxygen (DO), electrical conductivity (EC), salinity (Salt), and pH showed an upward trend, while CO₂ and CH₄ fluxes decreased during the experiment period. Significant differences in environmental factors and greenhouse gas fluxes were observed over time (p<0.05), but no significant differences were found between the treatment groups at the same sampling time (p>0.05). Warming increased the values of water temperature (WT), EC, Salt, and pH, while it suppressed DO concentrations. Nitrogen input decreased the values of WT and DO, but promoted the increases of EC, Salt, and pH. During the study period, CH₄ flux ranged from −14.16 to 90.53 mmol/(m²·d), and CO₂ flux ranged from −2 520.12 to 2 218.05 mmol/(m²·d). Overall, the lake ecosystem acted as a source of greenhouse gas emissions. The CO₂ and CH₄ exchange processes at the water-air interface were mainly influenced by WT, pH, and DO. pH was significantly negatively correlated with CO₂ flux (p<0.01), while WT and DO showed significantly positive correlations with CH₄ flux (p<0.01) and negative correlations with CH₄ flux (p<0.001), respectively. Warming did not directly affect CO₂ and CH₄ fluxes but promoted their emission by increasing WT. Nitrogen input significantly promoted CH₄ emissions (p<0.05). Both warming and nitrogen input inhibited CO₂ emissions by increasing pH. Overall, the interaction between warming and nitrogen input complicated the CO₂ and CH₄ exchange at the water-air interface. In conclusion, this study enhances the understanding of greenhouse gas emissions in shallow lakes, and provides scientific support for the management of eutrophic lakes in the context of global warming.