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All Organization face with important issues like objectives, constraints, priorities, policies, opportunities and threats that should be considered in all the key decisions. One of the most important and difficult decisions in organizations, is the project portfolio selection. In today's changing world, survival and continued growth of successful companies depends on developing and manufacturing  new products and services; as a result, Project Portfolio Selection(specially R&D Projects) is critical and necessary for the survival of its business of enterprises. The main problems in the R&D Portfolio selection process can be found in the large number of qualitative and quantitative goals that are often incompatible, the inconsistency in the amount of resources available and in use, experience of managers and decision makers to balance the risk and the timing of projects and the delivery time, etc. In this article a Mathematical model with the disctinction of taking the integration of knowledge and intellectual capital into account is presented and Solved With NSLS, For verifying the proposed model a case study is performed to select the best R&D Project Portfolio for an International LCSI in Iran. The results of the case study that satisfactorily validates the outcome of the model is presented.