Free trade zones play an important role in the economic development of countries by attracting foreign investment and strengthening export-based production. In Iran, according to the Article 5 of the Act on the Administration of Free Zones, the trustee of the administration of each organizational zone is a governmental organization, which is one of the pillars of commercial companies. According to existing studies, Iran's free zones have not been very successful in achieving policy goals. One of the approaches that can improve and reform the performance of these areas is the legal pathology of the administrative organization of the mentioned areas. Over the past two decades, corporate governance has been the main model for studying the structure and rules of companies. The present study has tried to evaluate the structure and rules of governing the Free Zones Organization with the criteria of corporate governance. The findings of the study indicate that the design of the rules of management of the Free Zones Organization, is not in line with the criteria of corporate governance. In fact, the legal status of this organization is the product of a flawed integration of the broad tasks of governance with economic goals in the legislative process. Therefore, one of the optimization ways in this regard is to separate the governing powers from the managerial and business activities focused on economic development.