Abstract Due to rapid expansion of higher education institutions which resulted in problems including squeezing effect of education budget and decreasing of education quality, higher education began to pay more attention to operating performance. In administrative performance evaluation of higher education in the past, official power (evaluation) was used to evaluate operation structure of the school and measure the operating performance of achievement of the school through National Award of Quality. Viewing from the angle of operating performance, in order to obtain existence and sustainable development, the framework and Key Performance Indicators (KPI) of operating performance should be established as reference of administration of higher education. This study established operating performance Input-Process-Output framework of higher education through literature analysis. Four educators and experts were interviewed to know importance levels and execution levels of these indicators. Thirteen dimensions and 68 performance indicators were established as reference of empirical questionnaire to find out important levels and execution levels for performance indicators of each school and conduct analysis of difference between general university and technology institute. KPI of operating performance in higher education was established by regression analysis. Abnormal indicators were found out by performance control matrix and items which needed improvement were identified and strategies were proposed. Empirical study found that higher education paid much attention to intangible assets including educational mission and vision and executive leadership on input perspective, to teaching process on process perspective and emphasized on customer satisfaction on output perspective. Major differences between general university and technology institute was that general university focused on inviting doctors as teachers, standard operating process of administration and number of publications in major journals. However, technology institute paid more attention to practical experience, specialty and certificate of teachers which were consistent with practical situation. Since resource of a school is limit, KPI must be established. This study identified 13 KPIs as indicators for overtaking the competitors and sustainable operation through regression analysis. In addition, 21 indicators outside of performance control matrix which had high importance and low execution and resources should be increased to promote organizational competition. Result of this study provided precious information for evaluation of Department of Education which could also be regarded as reference for administration of schools. Operation of the performance indicators should be paid much attention so as to help the schools to control operating situation of the resources of management, invest the resources to optimal place, obtain optimal application of the resources and assist higher education institutions to pay attention to education quality, emphasize operating performance and promote advantage in competition of each school.