Eutrophication is prevalent in urban lakes; however, a knowledge gap exists regarding eutrophication influences on carbon dynamics in these ecosystems. In the present study, we investigated the carbon dioxide (CO2) and methane (CH4) concentration and diffusion fluxes in Lake Tangxun (the largest shallow Chinese urban lake) in the autumn and winter of 2022 and spring and summer of 2023. We found that Lake Tangxun served as a source of GHGs, with average emission rates of 5.52 ± 12.16 mmol CO2 m−2 d−1 and 0.83 ± 2.81 mmol CH4 m−2 d−1, respectively. The partial pressure of dissolved CO2 (pCO2) (averaging 1321.39 ± 1614.63 μatm) and dissolved CH4 (dCH4) (averaging 4.29 ± 13.71 μmol L−1) exceeded saturation levels. Seasonal variability was observed in the pCO2 and dCH4 as well as CH4 fluxes, while the CO2 flux remained constant. The mean pCO2 and dCH4, as well as carbon emissions, were generally higher in summer and spring. pCO2 and dCH4 levels were significantly related to total nitrogen (TN), total phosphorus (TP), and ammonium-nitrogen (N-NH4+), and N-NH4+ was a main influencing factor of pCO2 and dCH4 in urban eutrophic lakes. The positive relationships of pCO2, dCH4 and trophic state index highlighted that eutrophication could elevate CO2 and CH4 emissions from the lake. This study highlights the fact that eutrophication can significantly increase carbon emissions in shallow urban lakes and that urban lakes are substantial contributors to the global carbon budget.