The implementation of a three-dimensional viscous inverse design used for an axial compressor is introduced in this paper. The derivation process of the inverse design algorithm is also described in detail. Moreover, an improved blade update method and a modified relaxation factor are included to enhance the inverse design algorithm. The inverse design is built on an in-house inverse design module coupled with commercial Computational Fluid Dynamic (CFD) software NUMECATM. In contrast to analysis design, the pressure loading and the normal thickness distribution along the blade surfaces are prescribed during the process of inverse design. The numerical methods used to solve the flow field are verified using the experimental data of the transonic fan rotor NASA Rotor 67. A recovery test for the Rotor 67 is carried out to validate the developed three-dimensional inverse design tool. To explore the potential application of the inverse design system, it is then used to improve the aerodynamic performance of a transonic fan Rotor 67 and a multi-row compressor Stage 35 at a near peak efficiency point by reorganizing the pressure loading distribution on the blade surfaces.