Selenium deficiency associated with a high risk of many diseases remains a global challenge. Owing to the narrow margin between "nutrition-toxicity" doses of selenium, it is imperative to achieve accurate selenium supplement. Nano‑selenium (SeNPs) is a novel form of selenium supplement with low toxicity, but it could be trapped and removed by intestinal mucus, thus limiting its oral delivery. The mucus penetration of SeNPs is highly associated with interactions between SeNPs and mucin (the structural component of mucus). In this study, we selected four polysaccharides with different functional groups and molecular weights, i.e. chitosan oligosaccharide (COS), chitosan (CS), chitosan quaternary ammonium salt (HACC), and carboxymethyl cellulose (CMC) as templates to modify SeNPs. Then we systematically explored the non-covalent interactions between polysaccharides stabilized nano-Se (PS-SeNPs) and mucin, determined and examined mucus penetration behavior and mechanism of different PS-SeNPs by coarse-grained molecular dynamics simulations, both in vitro and in vivo. It could be observed that penetration of PS-SeNPs depends on their distinct surface properties and mucus pH conditions. COS-SeNPs with short oligosaccharide chains accumulated and bridged with mucin, hindering its mucus penetration at pH 7.4. While HACC-SeNPs with NH and N exhibited high binding affinity with mucin, inducing its mucus penetration. The negatively charged CMC-SeNPs diffused freely in mucus due to their electrostatic-repelled interaction and hydrophobic interaction with mucin. This study establishes a theoretical foundation for precise application of SeNPs in oral administration and offers valuable insights into the precise utilization of polysaccharides as tailored carriers of nanoparticles in mucus-covered tissues.