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The data size of school affairs information is larger, the update speed is faster, the complexity is higher, the university management information system needs to be designed to improve the ability of information management. Traditional university management information system design using embedded Basic Visual information management system architecture method, the system of information and the ability to deal with multi thread processing performance is not good. A design method of university management information system based on multi feature data mining and embedded Linux is proposed. Firstly, the overall design and file configuration of the management information system of the university management information system in the embedded Linux, and the function module analysis and the technical index description are carried out. Design of data mining algorithm based on phase space reconstruction and association feature extraction, and the useful feature mining and extraction of management information in universities. In data mining results are program loading and guide, software development and design of management information system in Colleges and universities, including the program loading module, data storage module, cross compile module and network communication module design, based on data mining of university management information system to improve the design. The experimental results show that using the system of university management information mining and access scheduling, with good reliability and man-machine interaction, system throughput performance and execution time overhead index has advantages.