The dose rate effects of anti-fuse FPGA was specifically studied for parts screening. The results of experiments showed that all of the test circuits were seriously disrupted by low level of transient γ radiation, but none of them had latch up effect in high level of radiation. The low level radiation damage was due to that the transient photocurrents had caused the disruption of logic functions of anti-fuse FPGA. Nevertheless, the resistance of programmable switches in sea-cells prevented the radiation induced latch up effect in anti-fuse FPGA. The study results showed that the circuits hardening design was the best method to increase radiation fault-tolerance of anti-fuse FPGA.