Whey protein is an important component of milk, but heat treatment during sterilization has a certain impact on the structure and properties of whey protein. Therefore, this study investigated the effect of different heat treatments on the denaturation degree, physicochemical properties and functionality of camel whey protein, which was separated from camel milk heat-treated under different conditions, 65 ℃/30 min, 85 ℃/15 s, 125 ℃/4 s and 135 ℃/4 s, after milk fat and casein precipitation. The results showed that whey protein treated at 65 ℃ for 30 min had the highest turbidity (0.14), particle size (0.24 μm), zeta potential (-9.54 mV), solubility (24.57 mg/mL), and relative content of α-helix (31%) as well as the lowest relative contents of β-turn (13%) and random coil (19%); the water-holding capacity (WHC), foaming capacity and emulsifying capacity were significantly increased by the heat treatment, which indicated that 65 ℃/30 min treatment resulted in the smallest denaturation degree of whey protein and improvements in its functional properties such as emulsifying capacity, foaming capacity, WHC and oil-holding capacity (OHC) without significantly changing its physicochemical properties. With an increase in the heating temperature, the particle size of whey protein under 85 ℃/15 s treatment was increased to 0.32 μm, and the solubility was reduced to 22.34 mg/mL, but its functionality was improved compared with that of raw milk whey protein.Treatment at 125 ℃ for 4 s or 135 ℃for 4 s led to a large number of whey protein denaturation, destroyed the secondary structure, increased the particle size and turbidity, decreased the solubility, and worsened the functional properties.