Oyster is a low-carbon animal food enriched with protein, glycogen, and trace minerals. Nano-nutrients are increasingly perceived as an unignorable part of foods. Here, simulated gastrointestinal digestion released a considerable amount of nanoparticulate nutrients from raw and cooked oysters. They were identified as glycogen monomers with size of 20–40 nm and their aggregates, as well as 6 nm-sized bare cores of ferritin containing iron and zinc (4:1, w/w). FITC-labeling and flow cytometry unveiled the efficient uptake of oyster glycogen by polarized Caco-2 cells via macropinocytosis and receptor-mediated endocytosis. Calcein-fluorescence-quenching assay revealed divalent-metal-transporter-1- and macropinocytosis-mediated enterocyte iron absorption from oyster ferritin. Zinquin-fluorescence flow cytometry and ex-vivo mouse ileal loop experiments demonstrated the ready intestinal zinc absorption from oyster ferritin via macropinocytosis, as well as the good resistance of oyster ferritin to phytate's inhibition on zinc absorption. Overall, our results offer a new insight into the digestive and chemical properties of oysters.