This study aims to examine the relationship between total quality management(TQM) practices and operational performance perceived by employees who are in different functional organization types, R&D function and Non-R&D function organization in manufacturing companies. Operational performance is defined as the degree of operation efficiency in the perspective of quality, delivery, and cost. Our study showed that the significant elements of TQM practice were different depending on functional organization types. In case of R&D organization, the categories of customer focus and process management were the strongest significant predictors of operational performance. Therefore, the optimal TQM practices for R&D organization can be obtained in consideration of customer focus and process management.