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Appropriate performance management system is essential to the collaborative operation of the supply chain. This paper presents a quantitative performance measurement system for the supply chain. From time, quality, cost, and flexibility perspective, performance measures at department, enterprise and supply chain level are proposed. The comprehensive evaluation model is selected in Cobb-Douglas form to reflect the indispensability of each perspective. The key features in human evaluation are uncertainty, inconsistency and dependency, thus a modified fuzzy analytic network process is adopted as the comprehensive method.