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In order to solve the problem of SoC reliability failure caused by feature size reduction of CMOS devices, a scheme which realize logic reconfiguration of fault circuit based on online programming function of eFPGA is proposed. The technical advantages of eFPGA and the working principles of JTAG areanalyzed. The typical communication baseband signal processing algorithms, such as FFT algorithm and FIR filtering algorithm, are selected as example to simulate the logic reconfiguration when communication baseband accelerator function fails. JTAG technology is used to reconfigure the interconnection, therefore the eFPGA replaces the structure of communication baseband accelerator to realize function self-healing. Simulation and verification results show that eFPGA has advantages in area and power consumption. This scheme can achieve the expected logic reconfiguration function and effectively improve the reliability and flexibility of system.