Agricultural heavy metal contamination can cause significant crop damage, highlighting the urgent need to mitigate its negative effects. Under Cd stress, selenium nanomaterials (Se NMs, 2 mg kg) can significantly improve Brassica chinensis L. root growth and vigor, enhance photosynthesis (31.4%), and increase biomass. Se NMs treatment also reduces Brassica chinensis L root and shoot Cd concentration by 67.2 and 72.9%, respectively. This reduction is mainly due to the gene expression of Cd absorption (BcITR1 and BcHMA2) which was down-regulated 51.9 and 67.0% by Se NMs, respectively. Meanwhile, Se NMs can increase the abundance of Cd-resistant microorganisms (Gemmatimonas, RB41, Haliangium, Gaiella, and Steroidobacter) in rhizosphere soil while also reducing Cd migration from soil to plants. Additionally, Se NMs also contribute to reducing ROS accumulation by improving the oxidation-reduction process between GSH and GSSG through enhancing γ-ECS (15.6%), GPx (50.2%) and GR (97.3%) activity. Remarkably, crop Se content can reach 50.8 μg/100 g, which fully meets the standards of Se-rich vegetables. These findings demonstrate the potential of Se NMs in relieving heavy metal stress, while simultaneously increasing crop Se content, making it a promising technology for sustainable agricultural production.