Abstract: In order to reduce the complexity of CIS structure design, which is caused by the distribution, expansibility and reusing of information system in modern enterprises and especially to solve the problem of data sharing and mutual operation in heterogeneous database, middleware technique has been applied to simplify the development of information system. By analysis of the needs of CIS and the introduction of middleware, a design plan which is bases on J2EE middleware technology CIS system structure is described by this paper. Especially heterogeneous conditions coexistence regarding the non-structural database and the structural database, through the design based on the Java technology of middleware model, has been implemented the heterogeneous database inter-operation.