Identity issue and thinking about identity are the most important issues in all fields of humanities such as philosophy, political science, sociology and theology. Each of these fields gives attention to individual, social, national and global identity of modern humans, appropriate to their interests and knowledge.Thinking about identity has more booms in the Islamic societies, because of community-oriented features of Islamic identity and strength of national identity in Muslim societies, so that we can identify a widespread range of Muslim identity thinker, from Ummah- oriented to nationalist. Imam Khomeini (RA) as a mystic jurisconsult and a revolutionary politician, paid attention seriously to the modern human identity and Islamic societies, and also pursued redefining Iranian identity in theoretical and practical levels.This article considers identity issue, and more accurately the problem of duality of Ummah identity or national identity, in the opinion of Imam Khomeini (RA), and believes that “Mysticism Fiqh” is the meta-theory or the general spirit of his works and ideas, and this is distinct from this matter that the structure and elements of his thoughts is based on Ummah- oriented nature, and in his view, among the elements of national identity by highlighting the element of religion in Iran, it is possible the reconstruction of Iranian identity based on religion. So, we have analyzed the mystical approach and religious policy of Imam Khomeini (RA) in connection with the identity issue and we find the nobility of “Ummah” in this discourse and other collective identities and their bases (race, language, history, etc.) are placed in the margins.