As a toxic azo anion dye, Congo Red (CR) in waste-water poses a potential threat to the environment and human health. An absorbent is often used for its removal, during which, however, the role played by the functional groups is still not fully understood. In this work, a boehmite aerogel with a specific surface area as high as 305 m2/g was successfully developed by a combined sol–gel and freeze-drying method, and its CR adsorption capacity reached as high as 1962 mg·g−1. The adsorption process was dominated by a chemisorption mechanism and could be well described by the Langmuir isothermal model. The combination of the density functional theory (DFT) calculations and experimental results suggested that the amino protonation was responsible for the additional enhancement of CR adsorption in an acidic medium. The adsorption process occurred via interactions between boehmite aerogels and the SO3 functional groups of CR. Additionally, the NH3 group resultant from the protonation of NH2 functional groups of CR in an acidic medium significantly enhanced the CR adsorption on the boehmite aerogels. This work not only developed an ultrahigh efficiency anion adsorbent for CR removal, but also provided a new strategy for the exploration of new adsorbents with further improved performance.