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In order to fulfill the requirement of high-performance computing system for software definition interconnected communication, a kind of multi-protocol controller architecture was designed. The architecture supported a variety of protocol specifications and software-defining heterogeneous architecture. The interconnections of Fiber Channel, Ethernet and SRIO were realized by embedding programmable hardware circuits. The work mode of multi-protocol controllers was managed by software definition, which meet the heterogeneous requirements of system applications. The multi-protocol controller of the thesis has been realized in the 40 nm process, that the measurements show that the performance and function satisfy the standard of the three protocols.