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In order to improve the level of medical technology, speed up the medical staff of medical information data analysis, the medical information data run more smoothly, reduce the data storage of space, need for medical information data storage system design. The current medical information data storage system of medical information data for storage, use FPGA to build the system hardware, on the basis of the hardware to medical information data storage, but in the process of storage, there is no clear the redundant data, leading to storage space is full, smaller capacity, has the problem of the normal medical information data is placed. For this, put forward a kind of medical information data storage system based on fuzzy processing design method. This method first source of health information data statistics, according to the data source to realize the hardware structure of medical data, then use mediation between the characteristics of medical information data in the similar data points for data clustering, clustering of medical information data storage, and finally by using the gaussian mixture model to analyzing characteristics of medical data redundancy, on the basis of the analysis results, using fractional Fourier transform to delete redundant medical information data, thus complete the medical information data storage based on fuzzy processing. The experimental results show that the proposed method increases the data storage capacity, reduces the redundant data storage, to speed up the medical information data storage, improved the precision of data storage, the research in the field development provides a strong basis.