Abstract: Turbulence flux variance similarity relation was studied and parameterization based on between the wind speed (＜18 m/s) normalized standard deviation and stability was proposed under different atmospheric stability conditions based on the long-term observation of eddy covariance system at the Bohe marine meteorological observation platform in the northern South China Sea. Air sea momentum flux was estimated with flux-variance method and compared with the observations of eddy covariance system observations for verification of the parameterization. The results show that the normalized standard deviation of velocity under different atmospheric stratification conditions satisfy the 1/3 similarity relationship. The estimation by flux-variance method is consistent with the eddy covariance measurements, and their correlation is higher under unstable atmospheric stratification condition than that under stable stratification condition. It is practical and reliable to estimate the momentum flux of air-sea interface in the coastal waters with the flux-variance method.