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Because of their high nutritional value, the demand for scallops is increasing year by year. In the process of improving people’s living standards, the ready-to-eat characteristics and dry sales characteristics of this product make its shelling process particularly important in the production process. However, the mechanism of ultra-high pressure shelling has not yet been clarified. Therefore, in-depth study of the structural change of the scallop connection interface is of vital importance to explore the mechanism of ultra-high pressure shelling and the development of intelligent equipment from the mechanical point of view. The obturator muscle fibers and the inner surface materials of the shell at the obturator muscle scar of the scallop at 100, 200 and 300 MPa were obtained for Raman spectrum, Fourier-transform infrared spectrum and scanning electron microscopy analysis. The results showed that under the pressure of 200 MPa, the degree of protein denaturation of scallop adductor muscle increased, the elasticity disappeared, and the fiber was stretched; The deformation of the organic plasma membrane connected by the inorganic–organic interface weakens the binding force of the interface material and increases the possibility of the composite interface failure. To sum up, ultra-high pressure can effectively weaken the interface adhesion of scallop organic-inorganic composite materials, and is one of the effective ways of shelling. The research results can provide a basis for the in-depth analysis of ultra-high pressure mechanisms and the development of intelligent equipment, and provide technical support for the realization of ultra-high-pressure industrial production.