The invention provides a method for quickly estimating a single-particle function interruption rate of a satellite-borne FPGA. The method comprises the following steps: calculating single event upsetsPM1 and PM2 of a target FPGA and a similar FPGA already running in orbit under a task orbit environment condition after the resource usage is considered, and calculating a structure complexity coefficient; calculating a function abnormality probability PF1 of the target FPGA in orbit due to a single-particle soft error by using the data of the similar FPGA in orbit in the case that no safeguard procedure is taken; determining a protection coefficient beta p of the target FPGA after taking safeguard procedures, and calculating a function interruption rate of the target FPGA; and when the function interruption rate of the target FPGA does not meet the design requirements, performing improvement until the function interruption rate of the target FPGA meets the design requirements. The methodprovided by the invention is of great significance for evaluating the system-level function interruption rate of a spacecraft, quickly finding weak links in single-particle protection, and quickly improving the design.