Microvibrations may affect the quality and yield of products in precision processes. Therefore, vibration control is essential for minimizing position errors and improving the quality of production. Conventional active vibration isolation systems (AVISs) do not consider the effect of inertia variation, such as the movement of the stage and manipulator, on the system. Variations in inertia are associated with rotational motion, and they require a change in the modeling of an AVIS. Owing to this change, the system may not be optimal and may become unstable because the gain value is close to the critical point of the system. This results in insufficient performance. To overcome these issues, in this study, active vibration isolation was evaluated with the aim of actively controlling an AVIS while considering the effect of inertia variation. The system used in this study consists of an adaptive linear quadratic Gaussian (LQG) controller with six degrees of freedom. The inertia of the entire system changes based on the position of a stage mover. This variation in inertia alters the model of the system. The model is updated using the LQG controller, and the performance of the controller is evaluated. The LQG controller is used to evaluate the followability and transmissibility of the AVIS. The feedback loop is analyzed using Nyquist plots to determine the correlation between inertia variation and robustness. As a result, the phase margin decreases to 40°or lower as the rate of inertia variation increases. When the model is updated, the Nyquist's path is included in the unit circle. The correlation between inertia variation and performance is analyzed using Bode plots. The correlation shows a difference of approximately 10 dB depending on whether the model is updated.