Marginal seas serve as hotspots for global carbon sink. Along with sedimentary organic carbon (OC) decomposition and subsequent burial, denitrification and anammox are two vital processes that remove anthropogenic nitrogen, during which denitrification consumes OC via nitrate respiration accompanied by CO₂, N₂ and N₂O production, while anammox is a climate-friendly autotrophic process. The net effects of sedimentary nitrate respiration on carbon sequestration and greenhouse gases production in marginal seas remain underexplored. Here we show that denitrification predominates nitrogen removal (average ~91%), in which ~3.7% flows toward N₂O, along the coast of China from subtropical to temperate. Temperature and organics govern the spatiotemporal pattern of denitrification and N₂O production. Basing on the empirical equation configured with organic nitrogen content and temperature, we derive seasonal sedimentary denitrification for China’s marginal seas. Annually, 4.4 ± 0.5 Tg nitrate (~41% of total nitrogen input from land) is respired via degrading 3.5 ± 0.3 Tg OC (20% of OC deposited) to produce 0.07 ± 0.03 Tg N-N₂O in shelf seas. This amount of N₂O equals 8.1 ± 3.0 Tg CO₂-eq yr^-1 and offsets ~60% of the air-sea CO₂ influx (13.5 ± 10.7 Tg CO₂ yr^-1), underlining that sedimentary nitrate respiration compromises the role of marginal seas as a carbon sink.