Base isolation proves to be an effective vibration control strategy for buildings. However, the base-isolation floor (BIF) may undergo substantial displacements. To improve the seismic performance of base-isolation system, this paper proposes a multi-performance economical optimization procedure (MPEOP) for exploring the optimal parameters of base isolation system with tuned inerter negative stiffness damper (BIS-TINSD) subjected to non-stationary seismic excitation. The simplified analysis model for BIS-TINSD is developed, followed by the formulation of the state-space representation. The non-stationary seismic excitation is represented as a stationary Gaussian process with a time-modulating function based on the Clough–Penzien spectrum, and combining the equations of motion with seismic excitation results in the augmented state-space representation of structure-damper-excitation, followed by the formulation of differential Lyapunov equation. The multi-objective performance economical index is proposed, in which the performance optimization objective is defined as a weighted combination of base isolation floor displacement and superstructure acceleration, and the economic optimization objective is set as the support stiffness. The Pareto optimal fronts (POF) are adopted to deal with optimal objectives. The examination of optimal design parameters is extended under real earthquake records. The results demonstrate the effectiveness of the MPEOP, and indicate the advantages of the BIS-TINSD compared with the inerter amplify damper (IAD) and negative stiffness inerter damper (NSID).