There are three methods for calculating the optimal level for spare part inventories in a MIME (Multi Indenture and Multi Echelon) system : marginal analysis, Lagrangian relaxation method, and genetic algorithm. However, their solutions are sub-optimal solutions because the MIME system is neither convex nor separable by items. To be more specific, SRUs (Shop Replaceable Units) are required to fix a defected LRU (Line Replaceable Unit) because one LRU consists of several SRUs. Therefore, the level of both SRU and LRU cannot be calculated independently. Based on the limitations of three existing methods, we proposes a improved algorithm applying marginal analysis on determining LRU stock level and genetic algorithm on determining SRU stock level. It can draw optimal combinations on LRUs through separating SRUs. More, genetic algorithm enables to extend the solution search space of a SRU which is restricted in marginal analysis applying greedy algorithm. In the numerical analysis, we compare the performance of three existing methods and the proposed algorithm. The research model guarantees better results than the existing analytical methods. More, the performance variation of the proposed method is relatively low, which means one execution is enough to get the better result.