The invention provides a method for storing spaceflight initialization data. The method comprises the following steps of S1, configuring initialization data according to the bit file format of a preset FPGA program to obtain a bit format file, wherein the initial position of the initialization data points to the head position of a second program memory during the configuration process; S2, converting the constructed bit format file into an MCS format file by using a special software; S3, loading the PROM program file of the second program memory into a commercial flash device for product debugging; S4, after the debugging is completed, burning the PROM program file of the second program memory into a first program memory to realize the solidification of a final state. According to the method, an XQR17V16 program memory is adopted instead of a traditional spaceflight special data memory UT28F25LV for initializing data memories, so that the storage capacity is improved by 64 times. Meanwhile, the cost is reduced by 10 times and the economic value is high. In addition, data can be modified in the debugging process, and the method is convenient to use.