For the feature that the anti-radiation ability of Commercial Off The Shelf(COTS) devices is poor, it must be hardened for aero application. Then Single Event Upset(SEU) hardened design is done for a Flash Field-Programmable Gate Array(FPGA), and the ground ions accelerated testing is performed to verify the hardened design measures. The test result shows that the upset section of hardened Block RAM(BRAM) module reduces nearly 2 orders of magnitude, and the upset section of hardened register module reduces 75%. It verifies the validity of the hardened measures. According to the orbits environment, the SEU rate is calculated, the SEU rate of hardened BRAM module reduces 4–5 orders of magnitude, and the SEU rate of hardened register module reduces 2–3 orders of magnitude. It provides guidance for on-orbit applications.