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Protein content, a vital component determining the nutritional quality of oysters, is unevenly distributed in different parts of oyster. In this study, the spatial distribution (visceral mass, mantle, gill, and adductor) patterns and structural characteristics of proteins, including water–soluble proteins (WSP), salt–soluble proteins (SSP), acid–soluble proteins (ASP) and alkali–soluble proteins (ALSP) of oysters (Crassostrea hongkongensis) were investigated with the amino acid analyzer, circular dichroism spectroscopy (CD), fourier transform infrared spectroscopy (FTIR), and fluorescence spectroscopy. The results showed that oyster proteins were mainly distributed in the visceral mass and mantle. The protein composition was WSP, SSP, ALSP, and ASP in descending order, which conformed to the ideal amino acid pattern. Variations in secondary structure, molecular weight distribution, and thermal denaturation temperatures of the oyster proteins were observed. SSP had wider bands (16–270 kDa) than those of ASP (30–37 kDa) and ALSP (66–270 kDa). Among the four proteins, the SSP of the mantle showed the highest thermal stability (87.4 °C), while ALSP of the adductor muscle had the lowest the lowest the peak denaturation temperature (Tm) (53.8 °C). The proportions of secondary structures in oyster proteins were different, with a higher proportion of solid protein β–folds, and the exposure of aromatic amino acid residues and disulfide bonds and the microenvironment in which they were located were also different.