A new efficient numerical method for three-dimensional hydrodynamic computations is presented and discussed in this paper. The method is based on the operator splitting method and combined with Eulerian-Lagrangian method, finite element method and finite difference method. To increase the efficiency and stability of the numerical solutions, the operator splitting method is employed to partition the momentum equations into three parts, according to physical phenomena. A time step is divided into three time substeps. In the first substep, advection and Coriolis force are solved using the explicit Eulerian-Lagrangian method. In the second substep, horizontal diffusion is approximated by implicit FEM in each horizontal layer. In the last substep, the continuity equation is solved by implicit FEM, and vertical diffusion and pressure gradient are discretized by implicit FDM in each nodal column. The stability analysis shows that this method is unconditionally stable. A number of numerical experiments have been performed. The results simulated by the present scheme agree well with analytical solutions and the other documented model results. The method is efficient for 3D shallow water flow computations and fully fits complicated configurations.