Carbon emissions from lakes are an important part of the global carbon cycle. However, the current research on the characteristics of carbon emissions from lakes in arid areas and their influencing mechanisms is seriously insufficient, which leads to great uncertainty in the estimation of global lake carbon emissions. In this study, three typical lakes in arid region of Xinjiang—Ulungur, Sayram and Bosten Lakes were selected as the research objects. Samples of gas, water and sediments were collected in spring and summer of 2023, respectively. The concentrations of carbon dioxide(CO₂) and methane(CH₄) in each lake were calculated, and the corresponding diffusive and ebullitive fluxes were estimated. Combined with water quality, meteorology, sediment carbon and nitrogen content and other parameters, the carbon emission size and influencing factors of typical lakes in Xinjiang were discussed. The results showed that all the three lakes were net emissions of CO₂ and CH₄, with average CO₂ and CH₄ fluxes of (26.8±28.5) and (0.39±0.25) mmol/(m²·d), respectively. Due to the comprehensive influence of carbon sources and water quality, the carbon emission fluxes of lakes had seasonal differences. The CO₂ fluxes in spring ((19.1±26.5) mmol/(m²·d)) was lower than that in summer ((31.9±28.5) mmol/(m²·d)), and the CH₄ fluxes in spring ((0.55±0.25) mmol/(m²·d)) was higher than that in summer ((0.27±0.17) mmol/(m²·d)). On this basis, the magnitudes of CO₂ and CH₄ emissions from the three lakes in the arid region of Xinjiang were 212.0 and 4.7 Gg/a, respectively. Compared with other climate regions, lake carbon emissions in arid areas of Xinjiang were relatively low. However, considering lake areas in global arid regions are big, the magnitude of carbon emissions needs to be comprehensively considered in the research on global lake carbon emissions.