Recently, the Civil-Military conflicts are rising in various fields, and the majority of these conflicts is regarding the relocation of military establishments and its management. Therefore, the Military regards conflict management as policy pending issue, but in most cases because it weighs largely on executing post-factum measures, there is much hardship in fundamentally resolving the conflicts. This research focuses on pointing out the problems in the current conflict management system by case studies of civil-military conflicts, and seeks to find solutions to resolve the conflicts in preventive conflict management. This research takes a close look at the case of the establishment of the Jeju Naval Base and the relocation of the Army Special Warfare Command to Icheon and conducts analysis at the planning stage and the decision making stage, and draws policy implications for the establishment of preventive conflict management system. Both cases have induced strong resistance from the local society in unilaterally proceeding with the military plans without any process of disclosing information. While multilateral consultative groups were formed during the decision making process in both cases, it was discovered that in the case of the relocation of the Army Special Warfare Command to Icheon, there has been intense level of discussions which resulted in shorter period of conflict and early settlement. The analysis shows that the establish of a preventive conflict management system and systematic approach is much needed in cases of civil-military conflicts.