Abstract: The interaction between natural and thermally modified bovine lactoferrin (LF) and α-lactalbumin (ALA) was investigated at pH6.5 in phosphate buffer. ζ-potential, turbidimetric method, dynamic light scattering, optical microscopy, fluorescence spectrum and infrared chromatography were used for characterization. The results showed that the ζ-potential values of thermally modified LF-ALA complexes were lower than that of natural LF-ALA complexes. Natural LF and ALA could self assemble to form nanoparticles with a maximum size of (35.24±0.82) nm. The thermally modified LF and ALA could self assemble to form supramolecular structure. By adjusting the concentration of ALA, submicrometer and micrometer particles could be obtained. The maximum particle size was (4.11±0.14) μm. The complexes of natural LF and ALA were spherical aggregates with uniform distribution, while the complexes of the thermally modified LF and ALA were large aggregates with uneven distribution. ALA enhanced the hydrophobicity of tryptophan residues in LF. ALA_25℃interacted with the C=O and C-N groups in the LF structural subunits. This study provides a theoretical basis for the construction of novel double protein self-assembly and understanding of the mechanism of double protein assembly.