Introduction: Recognizing problems is one of the most effective activities in the implementation and continuation of macro projects. The health system transformation plan, like any other plan, has faced problems and issues. This study was conducted with the aim of pathology of the implementation of the health system transformation plan. Methods: During sampling by targeted judgment methods and snowballs with 15 experts and experts active in the field of policy making and implementation of health system policies and managers and medical staff working in medical centers-education affiliated to Iranian universities of medical sciences Semi-structured interviews were conducted. The interviews continued until the data reached the theoretical saturation stage. Data extracted from the text of the interviews were analyzed using theme analysis method. Results: After analyzing and coding the data, the identified damages based on the three-pronged model in the form of three main themes: structural and process damages (8 sub-themes and 24 concepts), behavioral damages (4 subthemes and 14 Concept) and environmental damage (5 sub-themes and 21 concepts) were categorized. In total, the identified injuries were categorized into 3 main themes, 16 sub-themes and 59 concepts. Conclusion: It is suggested that the relevant authorities to improve the structural, behavioral and environmental (underlying) factors to increase the effectiveness of this plan to be useful in providing health and treatment of vulnerable groups in the country.