Indonesia's criminal law reform reached a monumental milestone through the shift from a colonial penal paradigm toward a modern, restorative, and human rights oriented national legal framework. However, this systemic transformation exposes a profound normative friction with jus military, where institutional integrity and operational readiness depend on a rigid disciplinary structure. The enactment of the New Criminal Code significantly transforms general penal policy, urgently necessitating a structural and conceptual harmonization with the Military Criminal Cod. This research aims to analyze the challenges of harmonizing the KUHPM with the New Criminal Code, examine the dichotomy between general and military penal systems, and evaluate its implications for military discipline. Employing normative legal research with statutory and conceptual approaches, the study reveals that the penal dichotomy creates legal fragmentation, particularly regarding the integration of novel penal sanctions, such as community service and supervision orders into the strict hierarchy of military justice. Furthermore, inconsistencies in general penal principles risk blurring the boundaries between purely military offenses and internal disciplinary infractions. Future harmonization policies must reconcile modern criminal law philosophy with the lex specialis doctrine and command hierarchy, ensuring human rights protections without compromising military discipline and operational readiness.