The present article aims at applying the model of structural functionalism in crises due to disorders in functions of Islamic Republic of Iran under Mir Hussein Musawi's government. In that period, the State's macro policy was based on distributive justice and political-economic centralization. Based on the functionalist model, crisis and disorder are mainly explainable by malfunction of political system. On the one hand, according to Islamic revolution's causes and ideals, as well as the constitutional law, the fundamental goals of Islamic Republic of Iran fall into three major categories of freedom, justice and independence, to which the crisis and instability are directly related. On the other hand, according to structural functionalism, the main functions and tasks of the regime are served along with pursuing those goals which contribute to crisis and instability.