A 3-D numerical formulation is proposed on the horizontal Cartesian, vertical sigma-coordinate grid for modeling non-hydrostatic pressure free-surface flows. The pressure decomposition technique and θ semi-implicit method are used, with the solution procedure being split into two steps. First, with the implicit parts of non-hydrostatic pressures excluded, the provisional velocity field and free surface are obtained by solving a 2-D Poisson equation. Second, the theory of the differential operator is employed to derive the 3-D Poisson equation for non-hydrostatic pressures, which is solved to obtain the non-hydrostatic pressures and to update the provisional velocity field. When the non-orthogonal sigma-coordinate transformation is introduced, additional terms come into being, resulting in a 15-diagonal, diagonally dominant but unsymmetric linear system in the 3-D Poisson equation for non-hydrostatic pressures. The Biconjugate Gradient Stabilized (BiCGstab) method is used to solve the resulting 3-D unsymmetric linear system instead of the conjugate gradient method, which can only be used for symmetric, positive-definite linear systems. Three test cases are used for validations. The successful simulations of the small-amplitude wave, a supercritical flow over a ramp and a turbulent flow in the open channel indicate that the new model can simulate well non-hydrostatic flows, supercritical flows and turbulent flows.