To accurately calculate the turbulent exchange coefficient, the contribution of multi-scale turbulent transportation needs to be considered, especially in the complex terrain of the coastal area. In September 2019, a comprehensive observation experiment on the offshore atmospheric boundary layer was carried out at the Yangmeikeng Ecological Monitoring Station and Sai Chung Gulf. Through scale decomposition, it is shown that the turbulent motion in the atmospheric boundary layer in the coastal area is affected by the underlying surface, such as that of the coastal land or the sea–land boundary. This is the main reason behind the phenomenon whereby different scales make different contributions to momentum flux. Different multi-scale characteristics of turbulent structures on the underlying surface affect the drag coefficient. Through wavelet transform and finite element method, the characteristics of the multi-scale flow structures produced by the complicated offshore terrain are analysed. It is found that large-scale flow structures enhance the pulsating intensity at the small scale, but the large-scale coherence characteristics are different from those at the small scale. In summary, in comparing these three sites, the flux exchange on the roof is greatest, followed by that on the tower. In the Gulf, the flux exchange is mainly dependent on small-scale structures, which are linked with the smallest values.