Based on the hydrodynamical feature and the theoretical velocity profiles of tidal flow and wind-induced flow in shal-low sea, a computational model is established for the first time, which can separate observed velocity into tidal velocityand wind-induced velocity by use of the least square method. With the model, not only the surface velocities of tidal flowand wind-induced flow are obtained, but also the bed roughness height is determined and the wind velocity above the wa-ter surface is estimated. For verification of the model, the observed velocity in the Yellow River Estuary and the laborato-ry test is separated, then it is applied to the Yangtze River Estuary. All the results are satisfactory. The research resultsshow that the model is simple in method, feasible in process and reasonable in result. The model is a valid approach toanalysis and computation of field data, and can be applied to separate the observed velocity in shallow sea; at the sametime, reasonable boundary conditions of the surface and bottom can be obtained for two- and three-dimensional numericalsimulation.