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With the development of enterprise-wide and cross-enterprise application integration and interoperation toward Web service, Web service providers try to not only fulfill the functional requirements of Web service users but also satisfy their nonfunctional conditions in order to survive in the competitive market. A hot research topic is how to configure Web services to meet their demand when the diversity of user requirements, distinction of service components' performance, and limitation of resources are considered. This paper builds a Web service configuration net based on Petri nets in order to exhibit Web service configurations in a formal way. Then, an optimal algorithm is presented to help choose the best configuration with the highest quality of service to meet users' nonfunctional requirements. Finally, the simulation results and related analysis prove the soundness and correctness of our model and algorithm.