The South Caucasus region, as part of Iran's civilizational sphere, is of geostrategic importance to the Islamic Republic of Iran beyond the equations related to state-nation relations and geographical borders. Among the countries of the South Caucasus, the Republic of Azerbaijan is of particular importance to Iran in terms of its size, population, natural resources, extensive border with Iran, Shiite religion, Azeri ethnicity, and cultural and civilizational issues. Despite the great potential for convergence and cooperation between the two countries, the instability of bilateral relations has been the main characteristic of the relations between the two countries throughout the history of more than 30 years of relations. The Islamic Republic of Iran and the Republic of Azerbaijan are two neighboring countries with high cultural similarities that have been in an unstable atmosphere of bilateral relations due to numerous factors. The two countries have many aspects of interaction in bilateral relations in such a way that the scope of issues involved in bilateral relations is very large and diverse and covers a range of political, cultural, economic, military, environmental, and social issues. Therefore, managing bilateral relations in such conditions is very difficult. In this study, an attempt has been made to examine the effective roots in the convergence and divergence of the two countries by applying the theory of layered analysis of causes and to present suggestions for improving bilateral relations. The approach of this research is descriptive-analytical, its method is qualitative and the method of collecting information is library.