The controlled release of selenium nanoparticles (SeNPs) is pivotal significance in improving bioavailability and mitigating potential side effects. Three types of SeNPs, Selenium nanoparticles synthesized by chemical method (CSeNPs), extracellular polysaccharide-encapsulated selenium nanoparticles (EPS-SeNP), and selenium nanoparticles synthesized by Lactiplantibacillus plantarum (LacSeNPs), were synthesized in this study using chemical reduction, polysaccharide-assisted, and microbial reduction methods, respectively. The selenium release kinetics of the nanoparticles were investigated in simulated gastrointestinal with five kinetics models. CSeNPs released 67.80% of selenium in simulated gastric fluids (SGF) and, depicting a Brownian motion fraction of 81.0. EPS-SeNPs released 77.38% of selenium in SGF while only releasing 16.28% in simulated intestinal fluids (SIF). The release process was primarily affected by changes in the nanoparticle structure after Super Case II Transport in SGF and the zero-order model in SIF. The zero-order model provided the best fit for releasing LacSeNP profiles in the SGF. In SIF, the release mechanism of LacSeNPs was regulated by combination of diffusion and carrier swelling or erosion, leading to non-Fickian diffusion. Therefore, synthetic nanoparticle methods determine their structures and compositions, leading to differences in their release kinetics and release mechanisms. Notably, the release of LacSeNPs in the SGF aligns with the absorption patterns of selenium within the human body. The current study elucidates the potential application advantages of SeNPs synthesized using microbial means as selenium-enriched supplements.