A preconditioned method with characteristic boundary conditions for Navier-Stokes equations is implemented for flowfield analysis of a high-lift configuration at low Mach number. A preconditioned Harten-Lax-van Leer-EinfeldtWada scheme is adopted for the spatial discretization, and the dissipation term of which is rededuced to reduce the overlarge numerical dissipation. Preconditioned characteristic boundary conditions for the far field are derived based on the Weiss-Smith preconditioner and are demonstrated to be more reliable and accurate when coupled with the preconditioned method. A preconditioned Lower-Upper Symmetric Gauss-Seidel implicit time-marching method is modified according to the preconditioned Jacobian matrix. The applications of the current method on both two-and three-dimensional high-lift configurations indicate that the use of the preconditioned spatial and time discrete schemes and the derived preconditioned characteristic boundary conditions is capable of improving the robustness, efficiency, and accuracy of the computational-fluid-dynamics solver for low-Mach-number aerodynamic simulations.