This study is concern with the design of experiment planning for quality improvement in flow shop manufacturing system. In this study, the procedure of two stage experiment planning are proposed and applied to the manufacturing process of Li/$MnO_2$ batteries. The result of in this paper is that, compared with the current process conditions, 52% of the insulation inspection process, 81.6% of the first premier discharge process, 98.5% of the second premier discharge process, 84.7% of O.C.V./C.C.V. process, and 86.2% of voltage inspection process are decreased. After a given period of time, the life of the batteries extends to 75 hours, which means the 15% improvement in capacity. In case that the proposed methods are applied to the process Improvements of the flow shop manufacturing system, the much effected in experimental cost- saving and quality improvement.