Abstract: The purpose of this study was to explore the differences of protein and amino acid content, protein nutritional value and comprehensive quality evaluation based on amino acid content of three common oysters, Crassostrea sikamea, Crassostrea hongkongensis and Crassostrea ariakensis in Beibu Gulf. The content of protein in oyster was determined by national standard, and the composition and content of amino acids in oyster were determined by high performance liquid chromatography. The nutritional value of protein was evaluated, and the composition and content of amino acids in oyster were used as indexes for principal component analysis (PCA). The results showed the crude protein content (in dry basis) of Crassostrea sikamea, Crassostrea hongkongensis and Crassostrea ariakensis in Beibu Gulf was 43.47~49.27 g/100 g, and there were significantly differences among the three species. 17 kinds of amino acids were detected in three kinds of oysters, and the essential amino acids accounted for 30.95%~37.39% of the total amino acids, among which the essential amino acid composition of Crassostrea sikamea conformed to the ideal model recommended by FAO/WHO. The nutritional value of oyster protein was evaluated by amino acid score and chemical score. The results showed that Crassostrea sikamea and Crassostrea hongkongensis were more than 1 in AAS, the first limiting amino acid of Crassostrea ariakensis was leucine, the first limiting amino acid of Crassostrea sikamea and Crassostrea hongkongensis in CS was methionine+cysteine, and Crassostrea ariakensis was leucine. The protein nutritional value of oyster was evaluated by amino acid ratio coefficient, it was found that the protein nutritional value of Crassostrea sikamea was the highest among the three kinds of oysters, followed by Crassostrea hongkongensis and Crassostrea ariakensis. In PCA analysis, the cumulative contribution rate of the two principal components extracted was 90.463%, which could better summarize the comprehensive information of 17 amino acid evaluation indexes. The comprehensive score of the three oysters was Crassostrea sikamea>Crassostrea hongkongensis>Crassostrea ariakensis. This study provides a scientific reference for the development and breeding of three common oysters in the Beibu Gulf.