To develop an efficient and robust aerodynamic analysis method for numerical optimization designs of wing and complex configuration, a combination of matrix preconditioning and multigrid method is presented and investigated. The time derivatives of three-dimensional Navier-Stokes equations are preconditioned by Choi-Merkle preconditioning matrix that is originally designed for two-dimensional low Mach number viscous flows. An extension to three-dimensional viscous flow is implemented, and a method improving the convergence for transonic flow is proposed. The space discretizaition is performed by employing a finite-volume cell-centered scheme and using a central difference. The time marching is based on an explicit Runge-Kutta scheme proposed by Jameson. An effficient FAS multigrid method is used to accelerate the convergence to steady-state solutions. Viscous flows over ONERA M6 wing and M100 wing are numerically simulated with Mach numbers ranging from 0.010 to 0.839. The inviscid flow over the DLR-F4 wing-body configuration is also calculated to preliminarily examine the performance of the presented method for complex configuration. The computed results are compared with the experimental data and good agreement is achieved. It is shown that the presented method is efficient and robust for both compressible and incompressible flows and is very attractive for aerodynamic optimization designs of wing and complex configuration.