Shift feeling is one of the most important factors in developing a manual transmission. When drivers operate a manual transmission vehicle, they experience shift feeling which is classified into several factors such as shift smoothness, clarity, comfortability, sportiness, and so on. In the factors, shift smoothness characterized by double bump force is regarded as one of the most important things in experiencing shift feeling in Europe. The double bump force is reduced by attaching a constant mass damper which creates larger inertia of shift lever in control system of manual transmissions. However, it is possible to have side effects such as vibration of shift lever and clonk noise when employing the constant mass damper. In this research, a new control system with a variable inertia mechanism is designed and investigated to improve shift feeling while minimizing the side effects. The variable inertia mechanism is allowed to change inertia of the shift lever with respect to rotational angle of control shaft using a kind of lever mechanism. The change of the inertia is determined from motion of equation of the mechanism and also angular momentum of shift lever is calculated. Optimization method is employed to find out joint points of the new control system. Then, total mass of inertia body is minimized while amount of the change of the inertia is maximized. The shift feeling of a manual transmission with the new control system was verified by employing the previously developed shift feeling simulator and performing the vehicle test.