Variable cylinder management is fuel efficient technology enhancing both economic and environmental performances and is being adapted by various internationally recognized companies such as HONDA. With the use of Variable Cylinder system, the purpose of this study is to control and maintain the vibration characteristics when the number of operating cylinders are changing from 6 to 3. In order to achieve this goal, a novel adaptive algorithm based on Filtered-X LMS algorithm is proposed. Further, a suitable location of active engine mounts on the chassis in order to control and minimize the heave, longitudinal and lateral motions at the driver’s head rest position is found out by defining the new objective function. A reasonable amount of control effort of both the actuators has been reduced at optimal location. . Lastly, a comparison has been performed between two and three actuators cases and it can be seen from the simulation results that the performance has been improved however, power consumption in case of three actuators has been increased. Therefore, there is a kind of trade-off situation between the performance and the power consumption.