Backgrounds: Selenium (Se) as one of the essential trace elements for human plays an important role in the oxidation reduction system. But the high toxicity of Se limits its application. In this case, the element Se with zero oxidation state (Se0 ) has captured our attention because of its low toxicity and excellent bioavailability. However, Se0 is very unstable and easily changes into the inactive form. By now many efforts have been done to protect its stability. And this work was conducted to explore the antioxidant capacities of the stable Se0 nanoparticles (SeNPs) stabilized using chitosan (CS) with different molecular weights (Mws) (CS-SeNPs). Results: The different Mws CS-SeNPs could form uniform sphere particles with a size of about 103 nm after 30 days. The antioxidant tests of the DPPH, ABTS, and lipid peroxide models showed that these CS-SeNPs could scavenge free radicals at different levels. And the 1 month old SeNPs held the higher ABTS scavenging ability that the value could reach up to 87.45 ± 7.63% and 89.44 ± 5.03% of CS(l)-SeNPs and CS(h)-SeNPs, respectively. In the cell test using BABLC-3T3 or Caco-2, the production of the intracellular reactive oxygen species (ROS) could be inhibited in a Se concentration-dependent manner. The topical or oral administration of CS-SeNPs, particularly the Se nanoparticles stabilized with low molecular weight CS, CS(l)-SeNPs, and treated with a 30-day storage process, could efficiently protect glutathione peroxidase (GPx) activity and prevent the lipofusin formation induced by UV-radiation or d-galactose in mice, respectively. Such effects were more evident in viscera than in skin. The acute toxicity of CS(l)-SeNPs was tenfold lower than that of H2SeO3. Conclusions: Our work could demonstrate the CS-SeNPs hold a lower toxicity and a 30-day storage process could enhance the antioxidant capacities. All CS-SeNPs could penetrate the tissues and perform their antioxidant effects, especially the CS(l)-SeNPs in mice models. What's more, the antioxidant capacities of CS-SeNPs were more evident in viscera than in skin.