In our previous research, the modified Galerkin method was proposed as one of the most efficient methods for the analyses of convection-diffusion problems and two-dimensional viscous fluid flow problems. In this modified Galerkin method, the inertia term is considered explicitly, so only the symmetrical matrixes appear. Then an artificial viscosity is introduced through an error analysis approach to improve its accuracy and stability. In this paper, we proposed a new finite element formulation for three-dimensional incompressible viscous fluid flow analysis. This formulation (‘MS’ algorithm and ‘MSR’ algorithm) is based on the modified Galerkin method coupled with the Semi-Implicit Method for Pressure-Linked Equations. The cubic cavity flow problems were investigated for the Reynolds number of 400, 1,000, 2,000 and 3,200 using non-uniform meshes. Finally, we confirmed the effectiveness of our proposed method through the comparison with other research works.