The viscous simulation of civil aircraft wing-body-fairing is performed. Third-order upwind-biased implicit flux-difference splitting (FDS) and the implicit approximate factor decomposition (AF) are used to discrete and solve the three dimensional unsteady Reynolds Averaged N-S equations. The computation results match the wind tunnel experiment results well. And the viscous separation flow of wing-body trailing edge conjunction can be effectively simulated. Therefore these algorithms are valuable for the engineering applications.