In the present study, the potential of soy protein isolate (SPI)–κ-carrageenan (κ-CG) complex as a protective carrier for quercetagetin was investigated at different pH values (pH2.3 and 6.5). The particle size of the ternary aggregates was slightly increased at pH2.3, yet dramatically decreased at pH6.5 with increasing quercetagetin concentration. Moreover, the negative ζ-potential of the ternary aggregates was increased significantly (p<0.05) at pH6.5. The addition of quercetagetin to the SPI–κ-CG complex could highly quench the intrinsic fluorescence of SPI. Circular dichroism spectra further suggested that the bound quercetagetin could induce the rise of β-sheet and β-turn contents at the cost of α-helix and unordered coil fractions of SPI. In addition, quercetagetin could increase the viscoelasticity of the ternary aggregates at both pH. Furthermore, the SPI–κ-CG complex was found to be superior to single SPI or κ-CG in terms of improving light stability and radical scavenging ability of quercetagetin.