Life activities such as bioturbation and excretion of benthos affect nutrient content and migration at the sediment-water interface. The effects of Sinonovacula constricta bioturbation and its ammonia excretion on nitrogen nutrients in overlying water were studied based on a laboratory experiment in this study. Three treatment groups and a control group were set up according to different biological densities (63.66 ind/m²、127.32 ind/m²,190.99 ind/m²), and a 25-day laboratory experiment was carried out in the conditions of water temperature 23℃, salinity 22, and pH 8. The overlying water was collected every 5 days for analyzing the nitrogen nutrients and flux. The results show that the bioturbation of S. constricta. promoted the content of NH₄⁺ and NO₃^-+NO₂^- in the overlying water. With the increase of the density, the NH₄⁺ content increased obviously, while the content of NO₃^-+ NO₂^- increased first and then decreased. The NH₄⁺ flux is -0.195-0.273 mmol/(m²·d), that is, the ammonia nitrogen in the sediment is released into the overlying water. And the NO₃^-+NO₂^- flux is from -0.554 to 0.038 mmol/(m²·d), indicating that the sediment absorbed nitrate nitrogen from the overlying water. Considering the effect of ammonia metabolism of S. constricta. the ammonia nitrogen content was checked by ammonia data. Although the NH₄⁺ content decreased slightly, but the trend with time did not change. In addition, the NH₄⁺ flux changed greatly in the initial stage of the experiment, and it changed from sediment to overlying water release to migrate from the overlying water to the sediment, and then stabilized without obvious changes. Therefore, the bioturbation of S. constricta promoted the exchange of nitrogen nutrients between the sediment and the overlying water. The ammonia metabolism has a great influence on the flux in the early stage of the experiment, and the effect of ammonia metabolism gradually decreases over time.