According to the definition of integrated supply chain performance, improved method of grey relational evaluation and multi-level dynamic fuzzy comprehensive evaluation method are adopted to comprehensively evaluate the overall performance of the integrated supply chain. Based on these, the Performance Evaluation System (PES) of the integrated supply chain is developed on MATLAB software platform. In the end, the validity and feasibility of the system is validated by an example, and the system can provide a convenient operation tool and scientific, objective decision basis for managers to evaluate the integrated supply chain performance.