The Iranian criminal law system, by simultaneously utilizing the sources of Islamic jurisprudence and modern customary considerations, faces fundamental conflicts in the field of criminalization. This study, using a descriptive-analytical method and analyzing objective examples such as the criminalization of apostasy, drinking alcohol, and restrictions based on secondary rulings, has examined the foundations and manifestations of the conflict between jurisprudence and customary law. The findings show that in many cases, traditional jurisprudential rulings have been the basis for criminalization without a precise assessment of social necessity, criminal proportionality, and human rights standards. This situation has led to a conflict between jurisprudential rules and modern legal principles such as human dignity, privacy, freedom of belief, and the principle of legality of crime and punishment. In this regard, the study proposes solutions to reduce this conflict by analyzing the theories of "purposes of Sharia", "grounded ijtihad," and "Islamic human rights." Also, the role of institutions such as the legislator, the Guardian Council, and the Administrative Court of Justice in reforming legislative procedures and creating a balance between jurisprudence and custom has been analyzed. The conclusion of the research indicates that only by combining jurisprudential rationality with social and legal requirements can a coherent, legitimate, and efficient criminal system be achieved. Finally, this article emphasizes the need to review the foundations of criminal legislation and strengthen interdisciplinary dialogue between jurisprudence, law, and criminology.