Organizational structure plays an important role on survival of any business units and it is important to understand different factors influencing it. In this paper, we present an empirical study to learn the effects of three parameters including formality, concentration and complexity on organizational performance. The proposed study of this paper is implemented for one of research-based organization located in city of Qom, Iran. There were 120 employees working for this organization and the proposed study of this paper has selected a sample of 100 people, designed, and distributed a questionnaire among them. The proposed study uses two methods of regression analysis as well as structural equation modeling to study the impacts of three variables on organizational performance. The results show that there are some positive and meaningful relationship between formality and concentration from one side and organizational performance from the other side. In addition, there is a meaningful and negative relationship between complexity and organizational performance. The results of structural equation modeling are also consistent with the results of structural equation modeling.