Harmonization of the National Criminal Code and the New Criminal Procedure Code is essential to realizing a fair, effective, and human rights-oriented criminal justice system in Indonesia. This study aims to analyze the alignment between substantive criminal law and formal criminal law in ensuring legal certainty, procedural fairness, and the protection of human rights. The research employs a normative juridical method using statutory and conceptual approaches. The legal materials consist of relevant legislation, legal doctrines, and scholarly literature concerning criminal law and criminal justice. The analysis focuses on the consistency between criminal offenses, criminal sanctions, law enforcement procedures, and the protection of the rights of suspects, defendants, victims, and other parties involved in criminal proceedings. Harmonization is necessary to prevent inconsistencies, overlapping provisions, and differences in interpretation that may lead to legal uncertainty in law enforcement. Furthermore, the integration of substantive and procedural criminal law should ensure that the exercise of state authority remains subject to the principles of legality, proportionality, accountability, and due process of law. Effective harmonization also requires law enforcement institutions to understand and implement the new legal framework consistently. This study argues that the alignment of the National Criminal Code and the New Criminal Procedure Code is a crucial step toward establishing a criminal justice system that balances the interests of the state, society, and individuals. Therefore, comprehensive legal harmonization is expected to strengthen legal certainty, improve the quality of criminal proceedings, and promote justice and human rights protection in Indonesia.