Abstract Seagrass meadows are pivotal in coastal carbon cycling and climate regulation, yet simultaneous measurements of CO2, CH4, and N2O fluxes, especially in tropical systems, remain scarce. Here, we present the first synchronized seasonal assessment of these three greenhouse gases (GHGs) fluxes across water‐atmosphere in a tropical seagrass meadow (Li’an Lagoon, China). The ecosystem acted as a source of CH4 to the atmosphere but absorbed substantially more warming potential in the form of CO2 and N2O, resulting in a net atmospheric carbon sink. Notably, N2O uptake offset 63%–243% of the warming potential from CH4 emissions. At the global scale, tropical seagrass meadows exhibit higher median CH4 emissions yet stronger N2O uptake compared to temperate systems, also constituting a net GHGs sink from the atmosphere, with N2O uptake contributing 38%–164% of this sink effect. These findings highlight the necessity of multi‐gas assessments to accurately evaluate the climate function of seagrass ecosystems worldwide.