The　Schizochytrium　protein,　extracted　from　byproduct　of　Schizochytrium　sp.　after　lipid　extraction,　was　isolated　and　hydrolyzed.　A　specific　calcium-binding　peptide　was　purified　from　the　hydrolysate　through　Sephadex　G-25　gel　filtration　chromatography　and　C18　reversed-phase　high-performance　liquid　chromatography　(RP-HPLC).　The　calcium-binding　capacity　of　the　specific　peptide　reached　up　to　136.68　+/-　4.6　g/mg.　The　amino　acid　sequence　was　confirmed　as　Ser-Ser-Val　(SSV)　with　a　molecular　weight　of　291.15Da　by　liquid　chromatography　electrospray　ionization　tandem　mass　spectrometry　(LC-ESI-MS/MS).　Fourier　transformation　infrared　spectroscopy　showed　that　the　major　binding　sites　included　oxygen　atom　from　carbonyl　group　and　nitrogen　of　amino　group　or　imino　group.　SSV-Ca　chelate　was　confirmed　to　be　a　neutral　molecular　by　Zeta　potential　analysis,　and　the　calcium　ion　was　surrounded　by　the　functional　chelating　sites　of　SSV.　In　addition,　thermogravimetry-differential　scanning　calorimetry　(TG-DSC)　and　calcium　releasing　assay　revealed　that　the　SSV-Ca　chelate　exhibited　excellent　thermal　stability　and　solubility　in　both　acidic　and　basic　conditions,　which　was　in　favor　for　calcium　absorption　in　the　gastrointestinal　tracts　of　humans.　The　findings　indicate　the　by-product　of　Schizochytrium　sp.　is　a　promising　source　for　making　peptide-calcium　chelate　as　a　dietary　functional　supplement.