Peanut protein isolate (PPI) was treated by high-pressure microfluidization (40, 80, 120, and 160 MPa) and/or transglutaminase (TGase) cross-linking. It was found that individual microfluidization at 120 MPa was more effective in improving the solubility, emulsifying properties, and surface hydrophobicity of PPI than at other pressures (e.g., 40, 80, or 160 MPa). Individual TGase cross-linking also effectively changed the physicochemical and functional properties of PPI. Microfluidization (120 MPa) or TGase cross-linking caused the unfolding of PPI structure, resulting in the decrease of α-helix and β-turns levels and the increase of β-sheet and random coil levels, as proved by Fourier transform infrared (FTIR) and circular dichroism (CD) spectra. Compared with individual treatments, microfluidization followed by TGase cross-linking significantly (p < 0.05) improved the emulsion stability during long-term storage (20 days). Moreover, the combined treatments led to looser structure of PPI and resulted in more obvious changes in physicochemical properties.