Agriculture and natural resources systems are dynamic and changeable and using flexible models like accreditation system is effective for evaluating its quality and performance. This can be used to aware and transparent based on what they have to develop the supervisory culture and determine their current status. Monitoring and assessment issue is a type of management processes that should be attend to ISO standards and Deming cycle model. Although these standards are more applicable for the private sectors, considering the varrious approaches in the govermental units that have multiple responsibilities from the production of seeds and seedlings to the sale of some products, understanding and implementing the correct and comprehensive  quality management requirements in which creates distinctive advantages. However, the accreditation model does not deal only with setting standards, but  has also analytical, advisory and improvement dimensions. The accreditation model consists of internal and external evaluation that  examines and analyzes all effective aspects in the activity and performance of a research unit in partnership with people inside and outside of the unit based on the existing realities of the country. Then, it gives suggestions to reduce the weaknesses and improve the strengths of the unit to show the effectiveness of the unit for the agricultural and natural resources system of the country. Therefore, the present paper investigates the effective factors in performance analysis and describes the internal assessment using domestic and nondomestic experiences including CGIAR and ISO standards.