The progress of industrialization has led to a notable elevation in selenium (Se) levels within aquatic environments, surpassing established thresholds and posing significant risks to both human health and ecological equilibrium. Chitosan (CS) exhibits considerable potential in mitigating waterborne pollutants owing to its nontoxic nature, cost-effectiveness, and the presence of abundant hydroxyl and amino functional groups along its backbone. However, its subpar mechanical and thermal stability, susceptibility to acidic dissolution, and challenges in recycling impede its widespread use in water pollution mitigation. To address the aforementioned issues, this study employs a liquid nitrogen-directed freezing process to synthesize chitosan aerogel, aiming to enhance the adsorption efficiency of Se(IV). Morphological and adsorption tests demonstrate that the compact and closely interconnected porous structure facilitates diffusion of Se(IV) into the aerogel, thereby enhancing its adsorption efficiency. The theoretical adsorption capacity of the CS aerogel for Se(IV) is 56.45 mg/g, surpassing that of numerous natural and composite adsorbents, with adsorption equilibrium achieved within 2.5 h. Moreover, the CS aerogel demonstrates substantial potential in remediating Se(IV)-contaminated wastewater and improving circulation stability. A series of characterization results demonstrate that the primary adsorption mechanism of the CS aerogel onto Se(IV) involves electrostatic interactions, complemented by hydrogen bonding between the amino and hydroxyl groups of the CS aerogel and Se(IV), thereby augmenting the adsorption efficacy. This study introduces innovative avenues for tailoring the functionality of 3D macroscopic materials to address the remediation of heavy metals in aquatic environments.