The total-dose irradiation damage effects and post-irradiation annealing behavior of Altera SRAM-based FPGA were investigated in order to assess the anti-radiation level of FPGA devices used in space. Different modules were used to achieve the function of frequency division, and output waveforms of distinct modules changed following the total dose and annealing time. As various programs have different modules, by comparing power currents varying with the total dose and annealing time of different programs, different modules accumulated dose and annealing time were discussed. At the same time, the cause and difference of power current restoration under various annealing temperature were analysed. In the end, high and low level voltages at the output terminal were measured, and their relations with accumulated dose and annealing time were analyzed. The experiment results show that the annealing of the positive oxide charges would cause the recovery of the power current under various annealing temperature. With the increasing of annealing time, the functional recovery is sudden while the recovery of power currents is gradual.