Given the many uncertainties that exist in the project environment, the use of risk management in large and complex projects, which increases the likelihood of achieving project goals, is a necessity. In this regard, one of the factors that is very important in the risk management process is to identify the risks associated with the project with the design approach of risk failure structure. If the structure of risk failure is appropriate to the situation of the organization, the type of projects and the organizational structure, risk management studies in the areas of planning and risk identification in a simpler, more effective and more reliable way. The purpose of this research is to present the design methodology and structure of risk failure for research and development pilot projects in a project-oriented industrial organization. In this article, first the main uncertainties related to the mentioned projects were identified, then through their development and with the help of scientific resources and using the questionnaire and interview method, 96 common risks in this type of projects were identified. Finally, based on the validation of the results, the importance of each group of risks was determined and the structure of risk failure was designed in five groups of technical and technological risks, cost and financing, project organization, procurement and contracts and risks outside the organization.