This study takes a Navy shipyard as a sample that has the characteristics of non-for-profit organization. By linking Balanced Scroecards and Data Envelopment Analysis, this study integrates performance evaluation system and helps the Navy shipyard plant to develop and implement its strategic targets. The findings of this study are as follow: 1. The slack varaible analysis of operational efficiency shows that the increase of productivity utilization and the decrease of fixed assets can significantly improve the operational efficiency. 2. The regression analysis shows that non-financial performance measurement indexes drive up the operational efficiency. 3. The control of material allocation and the increase of productivity utilization can enormous influence the operational efficiency of the sample plant.