The cost-effective removal of gaseous elemental mercury from coal-fired flue gas is crucial for environmental protection. In this study, nano amorphous selenium (nano-a-Se) adsorbent was recovered from desulfurization wastewater to remove Hg0 in flue gas. The results indicate that nano-a-Se has a high efficiency in the amorphous form with a saturated adsorption capacity of 2034.32 mg g−1. The Se utilization ratio of nano-a-Se reached 80% of the theoretical limit. Meanwhile, nano-a-Se exhibited high resistance to NO and SO2 poisoning. Moreover, the Hg0 removal mechanism of nano-a-Se was analyzed by experimental analysis and density functional theory (DFT) calculations. The results demonstrate that nano-a-Se can convert Hg0 into stable mercury selenide, a high-value by-product with little risk of mercury re-release. Therefore, nano-a-Se is expected to be a novel adsorbent with high efficiency in capturing Hg0, which can help realize the resource utilization of toxic elements from the environment.