In recent years, the Ministry of National Defense has taken a series of innovations in military affairs to achieve reduce costs and improve efficiency through reorganization and streamlining of staff. This study applied the UNISON decision framework embedded the decision-driven organization theory to build a decision making facilities for reorganization of the National Defense Comptroller, and used AHP (Analytic Hierarchy Process) to construct the fundamental objectives of reorganization and relationship among its means objectives. Finally, a systematic framework for reorganization decision of the National Defense Comptroller is presented. The results would be regarded as a consultation and reference while the National Defense Comptroller making decisions about its reorganization.