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Some people often think about ISO 9000 as a group of documents, or a set of interrelated ideas, principles and rules that only concerns with the conformity to the documents. The true aim of 9000 system to enhance customer satisfaction and enterprise performance is compromised, so its effectiveness is often being questioned. Therefore, this paper proposes a quality system evaluation methods based on the system and the process method. Quantitative method based on modern information technology is used to improve the effectiveness of the management system itself, and monitor the conformity of processes. The research indicates that quality management system (QMS) can be broken down into three-layered structure consists of process network, process and activity. A model for evaluation of effectiveness of QMS is established based on the three-layered structure of QMS. The comprehensive evaluation method based on GAHP is adopted for evaluation of QMS.