A new non-hydrostatic numerical model with the three-dimensional Navier-Stokes equations on structured grids was constructed and discussed. The algorithm is based upon a staggered finite difference Crank-Nicholson scheme on a Cartesian grid. The eddy viscosity coefficient was calculated by the efficient k-ε turbulence model. A new surface-layer non-hydrostatic treatment and a local cell bottom treatment were introduced so that the three-dimensional model is fully non-hydrostatic and is free of any hydrostatic assumption. The developed model is second-order accuracy in both time and space when semi-implicit coefficient is set to 0.5. The validity of the present solution algorithm was demonstrated from its application to the three-dimension channel flow and the wave propagation over a submerged bar problems.