The real-time structural changes of the molecular space conformation of myofibrillar protein microgels (MPM) after heat treatment (90 °C, 30 min) were analyzed by molecular dynamics simulation, and the structural properties and changes of MPM at the oil-water interface were analyzed by the combination of Raman spectroscopy and molecular dynamics simulation. The shift in the oil ratio had a major impact on the transformation of disulfide bonds within the protein molecule. Simultaneously, it caused tryptophan and tyrosine residues (I850 cm−1/ I850 cm−1 > 1) to become exposed, increasing the locations of amino acid residues in the protein that interact with the oil phase. HIPE with different oil phases influenced the change in spatial structural conformation of MPM, and there was a flexible structural change in the molecular space. The HIPE system, which was stabilized by 3.0 wt% MPM and 0.75 oil phase, exhibited a thixotropic recovery of >70 % and the highest elastic modulus G′ (822.14 Pa) based on the rheological behavior. It is expected to provide a theoretical basis for the development and utilization of high internal phase emulsion stabilized by microgel protein in food industry.