During the process of updating the FPGA program and display parameters of the LED display control system, unexpected situations such as power failure or incorrect erasure may be encountered, which can result in the system to fail to work. In order to improve the reliability of the system, the FPGA program backup and system self- recovery are studied in this paper. Firstly, the MultiBoot configuration principle of Xilinx Spartan-6 FPGA is introduced. Then, according to the requirements of FPGA program and display parameter setting, the flash memory multi-region program and display parameter backup storage method are studied through the hardware design. Through the detailed programming of the FPGA MultiBoot configuration module, automatic call backup, automatic judgment, and hot restart of the program are realized. Finally, the generation method of the FPGA main and backup program firmware files is introduced. By simulating the FPGA program update error, it is verified that the system could call the ICAP setting register to trigger the IPROG command, and make sure the FPGA hot start to call the backup program to reconfigure. As a result, the stability and reliability of the LED control system updating and display parameter setting process are met by the practical application of FPGA MultiBoot configuration.