Polymer chemistry, rheology and cytotoxicity of cysteine initiated S-S redistribution in cold-extruded whey protein (TWPI) molecules were investigated. The locations of disulfide bonds in whey protein isolate (WPI), WPI dried without being extruded (OWPI) and cold-extruded WPI (TWPI), Cysteine (Cys)-treated WPI (WPI-Cys), OWPI (OWPI-Cys) and TWPI (TWPI-Cys) were precisely analyzed using liquid chromatography electrospray ionization tandem mass spectrometry (LC/MS/MS) combined with pLink software approaches. The numbers of intermolecular disulfide cross-linked peptides identified in Cys-treated samples increased by 4, 6 and 1, respectively, in the order of TWPI-Cys, OWPI-Cys and WPI-Cys. Fourier Transform infrared spectroscopy (FTIR) showed cysteine treatment loosed secondary structure of protein samples. Meanwhile, size exclusion chromatography (SEC) assay demonstrated the extensive polymerization in TWPI-Cys. Furthermore, Cys-treatment decreased the gelling temperature of TWPI to 57 °C sharply. Cys-treated TWPI has 19.11 times storage modulus (G’) and 25.86 times loss modulus (G”) of Cys-untreated TWPI at 85 °C. Additionally, cell viability with Cys addition indicate modified whey proteins are not toxic to human umbilical vein endothelial cells (HUVECs).