Spare parts are one of the important components of the equipment comprehensive support system. Spare parts management plays a decisive role in achieving the desired availability with the minimum cost. With the equipment complexity increasing, the price of spare parts has risen sharply. The traditional spare parts management makes the contradiction between fund shortage and spare parts shortage increasingly prominent. Based on the analysis of the multi-echelon and multi-indenture spare parts support model VARI-METRIC (vary multi-echelon technology for recoverable item control, VARI-METRIC), which is widely used by troops and enterprises in various countries, the model is mainly used in high system availability scenarios. However, in the case of low equipment system availability, the accuracy and cost of model inventory prediction are not ideal. This paper proposed the multi-level spare parts optimization model, which is based on the demand-supply steady-state process. It is an analytical model, which is used to solve the low accuracy problem of the VARI-METRIC model in the low equipment system availability. The analytical model is based on the multi-level spare parts support process. The article deduces methods for solving demand rate, demand–supply rate, equipment system availability, and support system availability. The marginal analysis method is used in the model to analyze the spare parts inventory allocation strategy’s current based cost and availability optimal value. Finally, a simulation model is established to evaluate and verify the model. Then, the simulation results show that, when the low availability of equipment systems are 0.4, 0.6, the relative errors of the analytical model are 3.54%, 3.86%, and its costs are 0.52, 1.795 million ¥ RMB. The experiment proves that the inventory prediction accuracy of the analytical model is significantly higher than that of the VARI-METRIC model in low equipment system availability. Finally, the conclusion and future research directions are discussed.