One of the most important strategies in order to move toward a knowledge-based economy, decreasing different kinds of managerial and non-managerial challenges that organizations are faced, and also maintaining the current competitive advantages and creating new competitive advantages, is establishment and development of effective R&D departments. Although equipment, financial, and human resources are known among the most important factors in order to evaluate the rate of R&D departments' ability, all of these factors along with procedural and managerial weakness cannot provide value for corporation. In order to investigate more about this aspect of R&D projects, case study was adopted as our research method. In this regard, through comparison of theoretical achievements and current R&D process, its challenges by participating and a structural approach were identified and by using experts' comments were prioritized. In subsequent, strategies for dealing with identified challenges through some meetings have been designed and by presenting to experts have been authenticated. At last, based on achieved strategies, R&D project management process of E organization through collaboration with experts has been designed and by joint meeting with organizational stakeholders has been improved and tailored.