Level of repair analysis (LORA) is an important method of maintenance decision for establishing systems of operation and maintenance in the equipment development period. Currently, the research on equipment of repair level focuses on economic analysis models which are used to optimize costs and rarely considers the maintenance time required by the implementation of the maintenance program. In fact, as to the system requiring high mission complete success, the maintenance time is an important factor which has a great influence on the availability of equipment systems. Considering the relationship between the maintenance time and the spares stocks level, it is obvious that there are contradictions between the maintenance time and the cost. In order to balance these two factors, it is necessary to build an optimization LORA model. To this end, the maintenance time representing performance characteristic is introduced, and on the basis of spares stocks which is traditionally regarded as a decision variable, a decision variable of repair level is added, and a multi-echelon multiindenture (MEMI) optimization LORA model is built which takes the best cost-effectiveness ratio as the criterion, the expected number of backorder (EBO) as the objective function and the cost as the constraint. Besides, the paper designs a convex programming algorithm of multi-variable for the optimization model, provides solutions to the non-convex objective function and methods for improving the efficiency of the algorithm. The method provided in this paper is proved to be credible and effective according to the numerical example and the simulation result.