A new method for direct numerical simulation of incompressible Navier-Stokes equations is studied in the paper. The compact finite difference and the non-linear terms upwind compact finite difference schemes on non-uniform meshes in x and y directions are developed respectively. With the Fourier spectral expansion in the spanwise direction, three-dimensional N-S equation are converted to a system of two-dimensional equations. The third-order mixed explicit-implicit scheme is employed for time integration. The treatment of the three-dimensional non-reflecting outflow boundary conditions is presented, which is important for the numerical simulations of the problem of transition in boundary layers, jets, and mixing layer. The numerical results indicate that high accuracy, stabilization and efficiency are achieved by the proposed numerical method. In addition, a theory model for the coherent structure in a laminar boundary layer is also proposed, based on which the numerical method is implemented to the non-linear evolution of coherent structure. It is found that the numerical results of the distribution of Reynolds stress, the formation of high shear layer, and the event of ejection and sweeping, match well with the observed characteristics of the coherent structures in a turbulence boundary layer.