Abstract: With development of Internet，interoperability of heterogeneous systems becomes a new hot research field.In order to run on such an open and dynamic environment derived from the Internet，the software should be component-based，open and intelligent.On the other hand，agent oriented programming well suits the above requirements.This paper presents one interoperability architecture of heterogeneous systems based on mobile agent in order to provide integrated information retrieval of heterogeneous data sources for users.The architecture is in fact a multi-agent system.This paper designs an agent communication mechanism based on common sense ontology model to implement communication and collaboration of agents.Working mechanism of mobile agent in the architecture is also described.