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In order to meet the high-reliable requirement of configuration bitstream of SRAM-FPGA in system of on-orbit reconfiguration, a design and implementation of storage system mixed with 3-module redundancy and loop-check is proposed. The reliability of mixed storage system is derived in detail by Markov model, considering influences of permanent error and temporal error in the space-born equipments on orbit and of maintenance rate. The differential equitation group is presented as the solution of reliability of the system. With simulation in Matlab, the influenced of permanent error and maintenance rate on the reliability of the system are analyzed. The reliability of mixed storage design achieves 0.99 on orbit, which further proves that the proposed design is obviously superior to the traditional 3-module redundancy system.