The mixture of whey protein and isolated soy protein with maltodextrin as microcapsules wall material was adopted. The secondary structure constitution of these two kinds of proteins in the process of heating and spray drying together with maltodextrin were studied by Fourier transform infrared spectra. The result showed that both whey protein and isolated soy protein exhibited differences in the secondary structures. The rate of α-helix in whey protein decreased 1.9% and β-turn content of the protein remains virtually unchanged, β-sheet increased 8.19%, and random coil decreased 7.18%. At the same time the content of α-helix in isolated soy protein decreased 1.64%, the change of β-sheet is not obvious while β-turn increased 10.20% and random coil decreased 9.03%. Meanwhile, the amideⅠbands of these two proteins both shifted to the lower wave number direction, indicating that in the formation process of the microcapsule wall structure there are complex interactions between maltodextrin and proteins, and the hydrogen bonds which comes into existence are comparatively strong. With the help of scanning electron microscope, it was discovered that the surface is more smooth and integrated when the microcapsules wall material contains whey protein, which is high in alpha helix.