Objectives: The main purpose of this paper is to apply the value based management model (VBM) on performance management, especially in the linkage of incentive compensation system in nonprofit sector. Methods: The measurement of social economic value depends on the social return on investment (SROI) and the cost of capital. Hospital has its own social economic value when the SROI is greater than weighted average cost of capital. Certainly, hospital shows its comprehensive performance by social economic value. Data from a non-for-profit hospital was used for this case study. Results: The simulation result of a hospital case shows its good performance based on social economic value. The social economic value among 2004-2006 years were NT$267,156,624,415,812,888 and 1,197,115,669 dollars. Owing to the linkage among social economic value, performance management and compensation in the VBM system, management of the hospital has motivation to make good decisions for financial self-reliance of the hospital. Conclusion: The system of VBM facilitated the hospital executives to focus on long-term operating performance, instead of short-term profit by means of the creation of social economic value. When the design of performance compensation links up with the social economic value and performance indicators in different level of organization, the hospital executives were motivated to create social economic value.