Present paper, using a descriptive-analytical approach, is aimed to analysis the transformations in Bahrain and challenges and opportunities facing the national security of Iran. In order to achieve research objectives, present study employed Martin’s integrated approach in studying Middle East’s national security as theoretical framework and considering five independent variables (combination of military and non-military factors) to assess the effect of Bahrain transformations on position and security of Iran in the region. Results of study mention to some opportunities such as strengthen the geopolitics of Shia, expanding the influence of Islamic republic of Iran and development of Iran’s Islamic pattern, decrease the role and presence of opposition competitors, improve the selective approach of U.S.A and EU and challenges such as continuing the presence of U.S military in region, increasing of ethnic and religious tensions, conflict between regional Arab countries’ profits, intensification and continuing Iranophobia and Shiaphobia project.