To develop integrated and flexible MES (Manufacturing Execution Systems) based on Agency and SOA (Service Oriented Architecture), after the definition of agent, the hierarchical structure of manufacturing management-control system with three layers has been presented. The core layer is the MES layer which includes nine Function Agencies. Each Function Agency consists of four types of agents with different functionalities. In this architecture, the Web Service is adopted to realize the communication between agents and the Market Mechanism is adopted to serve as control for interaction behavior among agents. The objectives of this paper is to illustrate the architecture of integrated and flexible MES with the purposes of integrating legacy systems together with MES, response rapid to a fluctuating market, flexibility and reconfiguration of the MES, the function of detailed planning, and the approach how a web services-based SOA supports our MES.