To realize the isolation from the deleterious vibration source, it is essential to model the vibration's physical characteristic and then compensate for it in the control scheme. However, most current research studies of active isolator treat the vibration as bounded lumped blocks or linear fashions in the system analysis. Therefore, it unavoidably results in unsatisfying isolation in practical applications. In this paper, the modeling technique on multiple frequency vibrations is first developed to pave the way for the controller formulation. Subsequently, a novel adaptive compensation network is constructed, which aims to compensate for the vibration's physical property. In what follows, an adaptive neural controller is proposed for stabilizing the active isolation system. Guaranteed by the Lyapunov method, all signals in the closed-loop system are kept stable during the vibration suppression. Finally, the comparative results are presented to validate the proposed scheme's effectiveness.