Currently, in areas where the military is present, residents and municipal governments claim their property rights and living standards that go as far as opposing the installation of new units and the removal of existing military presence. Therefore, the military needs to reexamine their conflict management methods as huge defense budget losses, rising conflicts, and dwindling combat strength is expected to occur. Accordingly, the MND has established a comprehensive remedy by creating branches to exclusively deal with dispute resolution and capacity augmentation, and managing an integrated conflict resolution system. However, the anticipated effect, conflict prevention and assessment of actual conflict is not yet systemized or crystallized. Thus, this study attempts to derive the limitations of the current military-civilian conflict management system and seek remedies to the said limitations. In order to achieve this effect, we review the M-C conflict theory from the perspective of M-C relations and compare public conflict management system and M-C conflict management system to suggest a new M-C crisis control system. This research yielded a new M-C CCS under the framework of organization, procedure and education. From the organization dimension, we were able to compose a conflict management practice/council, conflict response system, and conflict element analysis system; from the procedural aspect, conflict task selection and management tailored to military organizational traits, and business cooperation protocol; from the educational dimension, conflict resolution training to strengthen the capacity of the working level staff. Preemptive M-C CCS will promote an omni-directional Smart and professional cooperation system, Synergy, Skill, successful Solution toward national defense policies, and the optimum national defense Service to the Korean people and hence realize the Government 3.0 paradigm.