Seasonal temperature changes have significantly affected microbial functional transformations and greenhouse gas emissions in ecosystems. Current studies have shown that there is a direct regulatory effect of temperature on microorganisms in plant-free systems. The lakeshore zone, as an important site for climate change response, is characterized by periodic water-level fluctuations that place sediments under different flooding conditions, profoundly affecting the sediment microenvironment and microbial activity. However, the effects of temperature on functional microorganisms in lakeshore sediments with different flooding conditions have not been well studied. In this study, we investigated the short-term effects of temperature on microbial denitrification in lakeshore sediments by simulating four types of flooding conditions, including non-flooded (NF), intermittent flooded (IF), alternating high and low water level flooded (HLF), and constant water level flooded (WF). The results showed that increasing temperature significantly increased the sediment N2 release rate and decreased the N2O release rate under each flooding condition. In terms of microbial metabolism, the effect of temperature on carbon metabolic pathways was variable: under NF and IF conditions, 15°C promoted glycolysis and pentose phosphate cycle activities, while 30°C produced inhibition; while under HLF and WF conditions, 30°C significantly activated different carbon metabolic activities. Meanwhile, the content of electron donors was inhibited by 30°C under NF and IF conditions, but significantly increased under HLF and WF conditions. Notably, temperature altered the electron-consuming capacity by modulating the activity of denitrification key enzymes, resulting in an increase in the N2 potential release rate and a decrease in the N2O potential release rate. In terms of microbial communities, temperature significantly altered the diversity and compositional characteristics of nirS and nosZ-type denitrifying bacteria in lakeshore sediments under different flooding conditions. Further analysis by partial least squares path modeling indicated that the community of nirS and nosZ-type denitrifying bacteria was a key indicator for predicting the potential release rates of N2 and N2O at different temperatures compared to the metabolic processes of microorganisms. In addition, by estimating the potential emissions of N2 and N2O from sediments in the lakeshore zone, it was found that sediments in the area of frequent water level fluctuations in the lakeshore zone have a better nitrogen removal capacity under high temperature (30℃) environments, which is a key spatial and temporal point for the conversion of greenhouse gases to the environmentally friendly end-product N2.