There is a strong real-time coupling between seabed topography and wave field, current field and wind field in shallow water area. The existing analysis model cannot directly consider the influence factors of seabed, and it is more difficult to explain the unsteady evolution mechanism of the coupling field between typical seabed topography and wave, shear flow and gradient wind. Based on the secondary development of STAR-CCM+platform, the shallow sea wind-wave-current numerical pool is constructed under four typical seabed landform conditions: seabed plain, seabed slope, trough, and flat landform. The multi-layer particle velocity coupling method is proposed and the multi-layer wind-wave-current coupling model is established. The wind-wave-current decoupling is realized at the initial time. The temporal and spatial evolution laws of wave field, current field, and wind field in different seabed topographies are compared and analyzed. The principal component analysis method is introduced to evaluate the unsteady effect of wind-wave-current in various typical seabed topographies, and the unsteady evaluation index of the whole life cycle of the wind-wave-current-seabed coupling field is established. The results show that the multi-layer wind-wave-current coupling model can more truly reflect the influence of vertical wind speed and uneven velocity distribution on wave field. The seabed topography can lead to a multi-stage time-history distribution of wave field in the evolution process. The flat topography, submarine slope, and trough conditions are divided into wave surface surge, attenuation, and stability stages. The submarine plain conditions are divided into external breaking wave, internal breaking wave, and climbing stage. The evolution of the current field presents a multi-stage spatial distribution, and the seabed leads to the formation of multi-vortex accumulation or multi-vortex coexistence in the current field. The coupling evolution of wind-wave-current-seabed has an amplification effect on the wind profile index, and positive relationship between seabed height and wind profile coefficient. The end-stage unsteady evaluation indices of flat landform, submarine plain, submarine slope, and trough are 0.268, 4.612, 0.672, and 0.926, respectively.