In order to reduce the comprehensive cost of military central warehouse to the maximum extent, optimize the location of its location, and select the best central warehouse from numerous military warehouses. Put forward the concept of comprehensive cost based on analytic hierarchy process (AHP), and with minimum cost as the objective function, optimization model was established by using the immune algorithm, determined the military center in the instance warehouse location problem by using Matlab software, and through the fitness curve to determine the fitness of convergence. The results show that the algorithm is simple and effective, and can provide efficient and effective logistics guarantee, which has a strong reference value for the military center warehouse site selection, and has a high value of promotion.