Aerospace industry is integrated with state-of-the-art technology but uncertainty is increasing due to the lack of accumulated data. In addition, projects at aerospace research and development institutions have become large and complex. Accordingly, the organization's top level has recognized the importance of risk-informed decision-making and performed risk management to operate the organization successfully. However, it is difficult to set the priorities of risk treatment as a whole in the aspect of managing risks of the organization because each project may have a difference in methods for the risk identification, assessment and determining risk levels. Thus, it is required to develop a standardized and quantitative method that can integrate risks in the level of each project to identify the status of risk management intuitively at the top level for all projects performed by the organization. This paper presents an index-based scheme for an organization-level risk management. To obtain the organization-level risk index, the risk index of each project is summed up by applying the weighting factors representing the priority of the project in the organization, such as budget. The risk index of each project is calculated by summing the levels of the risks and applying the weight factor according to the target schedule. The risk level is determined by probability and severity of the risks, which are calculated according to the quantitative evaluation standard. Based on this method, a risk model(R-Model) is established and applied to a research institute by using real data for 3years. By analyzing the trends of the index, it can be confirmed that R-Model helps intuitively identify risks and make decisions at the top level. This paper is significant in developing an index-based scheme for an organization-level risk management and validating the proposed scheme through a case study on real projects of a major aerospace research institute.