Radio frequency identification(RFID) is high technology, which can rapidly and real-timely acquisition information and accurately deal with information. And it has broad application prospects in retail, logistics, transport and other fields. Service oriented architecture(SOA) is a service-oriented architecture, which is used to design and realize the loose coupling software. For the existing shortcomings of current enterprise information system integration, the RFID technology and SOA are introduced into system integration in order to propose a new enterprise information system integration scheme in this paper. In the proposed system integration scheme, the middleware uses the business documents as the carrier of data exchange among other enterprise application systems, and the data stream technology is used to filter and package RFID data. The rule parsing technology is used to control the business processes. The SOA is used to realize the loose coupling and integration of RFID data event and application system, and deal with the configuration of the components. At the same time, .NET Remoting technology is used to realize the distribution architecture of middleware in order to ensure the deployment flexibility of middleware. The applied cases of a demonstrative application system, blood management and traceability system are used to illustrate its feasibility and effectiveness of the proposed integration scheme. The enterprise information system integration scheme provides an effective solution for system integration between different enterprises or internal enterprises. It can solve the compatibility between different application systems, and takes on the higher service efficiency, less CPU average occupation and better average response time. This study provides a stable and effective solution for information sharing between enterprises, improves the work efficiency and reduces the whole work management capital, and continuously improves the informatization level of the enterprises.