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Massive labile carbon and nitrogen inputs into lakes change greenhouse gas emissions. However, the rapid driving mechanism from eutrophic and swampy lakes is not fully understood and is usually contradictory. Thus, we launched a short-term and anaerobic incubation experiment to explore the response of greenhouse gas emissions and microbial communities to glucose and nitrate nitrogen (NO3−-N) inputs. Glucose addition significantly increased CH4 and CO2 emissions and decreased N2O emissions, but there were no significant differences. NO3−-N addition significantly promoted N2O emissions but reduced CH4 accumulative amounts, similar to the results of the Tax4Fun prediction. Bacterial relative abundance changed after glucose addition and coupled with the abundance of denitrification genes (nirS and nirK) decreased while maintaining a negative impact on N2O emissions, considerably increasing methanogenic bacteria (mcrA1) while maintaining a positive impact on CH4 emissions. Structural equation modeling showed that glucose and NO3−-N addition directly affected MBC content and greenhouse gas emissions. Further, MBC content was significantly negative with nirS and nirK, and positive with mcrA1. These results significantly deepen the current understanding of the relationships between labial carbon, nitrogen, and greenhouse emissions, further highlighting that labile carbon input is the primary factor driving greenhouse gas emissions from eutrophic shallow lakes.