Security as one of the most obvious governmental principles has always attracted the attention of governments, religious, political and military pundits whose absence makes the provision of other requirements impossible and has challenged the threats and inhibitors of this great boon. The mian objective of this article is to explain inhibitors and threats of national security in the thought system of Imam Khomeni. To do this, by studying the research history, a theoretical framework has been prepared and in regards to the type of research which is of applied and descriptive-analytical kind and using library and expert methods, data was collected from Imam Khomeini’s speeches through databased method which led to the extraction, perception and conclusion with a reliability average of 92 percent and justifiability and credibility of 94 percent on findings. Security inhibitors: damage, affliction, crises and threats in various dimensions, particularly political, cultural, economic, religious, legal and social ones were extracted and explained. The main fundamental threats to internal security are falsification, ruining undermining and limitation of religion which have led to crises of lack of legitimacy, capability, efficiency and acceptance.Suggestions have been presented to prevent affliction, damage and crises and methods to counter these threats to improve security capabilities of the Islamic Republic of Iran, as well. These suggestions include improving spiritual and religious basis of the society, doctrine measures of public welfare, popularizing internal security and authorities’ governance over hearts and not bodies.