In order to improve the harsh dynamic environment experienced by heavy rockets during different external excitations, this study presents a novel active variable stiffness vibration isolator (AVS-VI) used as the vibration isolation device to reduce excessive vibration of the whole-spacecraft isolation system. The AVS-VI is composed of horizontal stiffness spring, positive stiffness spring, parallelogram linkage mechanism, piezoelectric actuator, acceleration sensor, viscoelastic damping, and PID active controller. Based on the AVS-VI, the generalized vibration transmissibility determined by the nonlinear output frequency response functions and the energy absorption rate is applied to analyze the isolation performance of the whole-spacecraft system with AVS-VI. The AVS-VI can conduct adaptive vibration suppression with variable stiffness to the whole-spacecraft system, and the analysis results indicate that the AVS-VI is effective in reducing the extravagant vibration of the whole-spacecraft system, where the vibration isolation is decreased up to above 65% under different acceleration excitations. Finally, different parameters of AVS-VI are considered to optimize the whole-spacecraft system based on the generalized vibration transmissibility and the energy absorption rate.