The effects of dynamic ultra-high pressure homogenization (UHPH) on the structure and functional properties of whey protein were investigated in this study. Whey protein solution of 10 mg/mL (1% w/w) was prepared and processed by a laboratory scale high pressure homogenizer with different pressures (25, 50, 100, 150, 200, and 250 MPa) at an initial temperature of 25 °C. Then, the solution samples were evaluated in terms of secondary structure, sulfhydryl and disulfide bond contents, surface hydrophobicity, average particle size, solubility, foaming capacity, emulsifying activity, and thermal properties. It was found that the secondary structure of whey protein changed with the dynamic UHPH treatment. The interchange reaction between the disulfide bond and the sulfhydryl group was promoted and the surface hydrophobicity significantly increased. The functional properties of the whey protein accordingly changed. Specifically, after dynamic UHPH treatment, the average particle size of the whey protein and emulsion decreased while the solubility, the foaming capability and the emulsification stability increased significantly. The results also revealed that with the dynamic UHPH at 150 MPa, the best improvement was observed in the whey protein functional properties. The whey protein solubility increased from 63.15 to 71.61% and the emulsification stability improved from 195 to 467 min.