In order to improve their social and economic conditions, different societies need to provide grounds for growth and development, and one of the factors affecting the growth and development of any country is the transformation in the country's scientific structures. The research method of this article is descriptive-analytical and the data collection method is library and documentary. The purpose of this article is to identify and examine the obstacles to the scientific development of the Islamic Republic of Iran in the framework of the theory of neo-institutionalism. In this article, while examining the theory of neo-institutionalism, structural factors such as the multiplicity of decision-making centers in the matter of scientific development, a little look at researches and scientific articles, the structure of universities and the regulations for the promotion of professors, and political factors such as the influence of political tendencies in The selection of presidents of universities, faculties and professors, the policy of quantitative expansion of universities and the way of attracting students, especially in graduate studies, are mentioned as obstacles to Iran's scientific development. Reforming the decision-making structure and by-laws, along with avoiding factional and political views on scientific development and universities, as well as creating scientific and research poles, can provide the basis for the scientific development of the Islamic Republic of Iran.