Near-fault pulse motions will cause excessive and much larger base displacement in traditional isolated structures than common earthquake motions. The new isolation system inspired by the “sacrificial bonds and hidden length” biomechanics of an abalone shell can control the base displacement efficiently and reach almost the same vibration isolation efficiency as a semi-active control system. The current research is confined to the lumped mass model and cannot uncover the exact performance of isolators and structures in practical applications. A user subroutine is developed based on the interface of UEL in Abaqus. Subsequent verification has been done in both the lumped mass model and 3D complex model with Abaqus, Matlab/Simulink, and SAP2000. It can be revealed from the comparative results that the calculation accuracy of the secondary developed user subroutine can meet the demand of design and research.