In the article, have been researched the directions for the formation of the agricultural sector in the post-conflict region of the Republic of Azerbaijan, the economic importance of its sustainability through digital transformation, the main directions for the application of digital and innovative technologies and the analysis of potential problems and their solution directions. The article also discusses about the importance of interactions between different fields and the responsibilities of each field in the effective application of digital technologies in the agricultural sector. As a result of the conducted research, proposals were put forward regarding the implementation of the long-term digital transformation of the agricultural sector in Karabakh and Eastern Zangezur economic regions in Azerbaijan.