The work aims to explore the shelling mechanism of ultra-high pressure and study the structural changes of scallop shell connecting interface under ultra-high pressure to provide basic theory for industrial production of ultra-high pressure technology. The structure of mineral and organic matter in scallop shell under different ultra-high pressure was analyzed by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The results showed that the mineral structure in scallop shell was relatively stable under ultra-high pressure, but the structure of organic matter in shell and inner surface changed significantly. The intensity of each characteristic peak of infrared spectrum also had obvious difference. The contents of α-helix, β-fold, β-turn and irregular curl in the secondary structure of organic matter were also different. Especially under 200 MPa, the content of α-helix was the lowest, 20.12%; and the content of β-fold was the highest, 41.81%. This made the elasticity of organic matter decrease and changed the status of interface between shell and adductor muscle. Analysis on micro-structure of inner surface of scallop shell under different pressure showed that the continuity of the organic plasma membrane on the inner surface of scallop was changed, which made the stress distribution of the interface uneven and reduced the strength of the connecting interface, resulting in the failure of the interface between the adductor muscle and the shell. The study of the structural changes of scallop shell interface under ultra-high pressure can provide a certain research basis for further clarifying the shelling mechanism and even the action mechanism of ultra-high pressure.