To verify the feasibility of key performance indicators (KPI) evaluating model of public institution based on the analyzed results of KPI of Institute of Chinese Materia Medica of China Academy of Chinese Medical Sciences. Establishing KPI evaluating model according to scientific research characteristics of public institution. Indicators of flexibility can guarantee the dynamic adjustment with strategic goals of public institutions, and the accurancy and convenience of data collection. The KPI model of Institute of Chinese Materia Medica of China Academy of Chinese Medical Sciences has showed the justic and effecient for the work performance to motivate the staff. The KPI evaluating model has showed the good operability.