This paper aims to review and analyse the introduction process of performance management system(PMS) in the R&D sector. It also examines initial problems and future policy directions of the new system. Theory part deals with various approaches to the PMS and the relation between research evaluation and performance management. The paper then describes how the PMS has been introduced in the National R&D Program by the MOST in terms of the contents of strategic goal, performance goal and performance indicator together with their development process. After this, it captures problems arising in the initial phase and then suggests how they should be solved on the ministerial and cross-ministerial level. Discussed are following topics: lack of strategic planning, grouping of heterogeneous sub-programs, duplication between the OMS and other existing research or performance evaluation. The paper finally suggests policy implications using the logic model which has been developed in a series of recent international conferences.