Oysters are commercially important shellfish that produce large amounts of high-quality animal proteins. Crassostrea oysters are currently the only oyster species used in aquaculture. Little is known about the quantities and dietary properties of Hyotissa oysters or their breeding and aquaculture technologies. Hyotissa oysters are locally known as stone oysters and are popular on Weizhou Island, Guangxi. Unlike Crassostrea species, the adductor muscles are the main edible parts of Hyotissa oysters. The stone oysters include H. hyotis, H. inaequivalvis, and H. sinensis. The nutritional composition of the adductor muscles of H. hyotis in South Korea has been analyzed but not that of the stone oysters in China. We therefore collected wild stone oysters from Weizhou Island in Guangxi in August 2024 and determined the nutritional composition of their edible adductor muscles according to the national standards in China, i.e. GB 5009.3, GB 5009.4, GB 5009.5, GB 5009.6, GB 5009.124, GB 5009.168, and GB/T 9695.31. The quality of amino acids and fatty acids was assessed using indices, such as the amino acid score, chemical score, essential amino acid index, taste activity value, atherogenicity index, and thrombogenicity index. The results showed the following: 1) The contents of total ash, fat, and total sugar in the adductor muscles of the three Hyotissa species were comparable, at 2.16–2.43 g/100 g, 1.28–1.42 g/100 g, and 2.24–2.69 g/100 g, respectively. The protein contents were 13.68–16.99 g/100 g. 2) A total of 17 amino acids were identified in the adductor muscles of all three Hyotissa oysters, including 7 essential amino acids, 4 semi-essential amino acids, and 6 non-essential amino acids. The amino acid contents were similar among the three stone oyster species, except that the cysteine and valine contents in H. hyotis were substantially lower than those in H. sinensis, and the tyrosine content in H. hyotis as notably higher than that in H. inaequivalvis. The content of glutamic acid was highest among all amino acids in all three species (2.10–2.40 g/100 g), followed by aspartic acid (1.30–1.45 g/100 g). The cysteine content was lowest among the 17 amino acids, at 0.03–0.05 g/100 g. H. hyotis had the highest contents of three flavor amino acids (aspartic acid, glutamic acid, and alanine), as well as total, essential, non-essential, and semi-essential amino acids. However, the contents of these amino acids were comparable among the three stone oyster species. The essential to total amino acid ratio was almost 40%, and the essential to non-essential amino acid ratio was over 70% for all species. 3) The fatty acid compositions differed among the three oyster species. H. hyotis contained 15 fatty acids including 7, 5, and 3 polyunsaturated, saturated, and monounsaturated fatty acids, respectively. H. inaequivalvis and H. sinensis contained only 12 fatty acids. The total fatty acid content was highest and lowest in H. hyotis (414.24 mg/100 g) and H. inaequivalvis (355.64 mg/100 g), respectively. The C16:0 content was the highest among these fatty acids, followed by C18:0. The C20:2 and C20:3n3 were detected only in H. hyotis. 4) The amino acid and chemical scores were highest for lysine, and the first limiting amino acid was methionine+cysteine. Lysine in H. hyotis, leucine and lysine in H. inaequivalvis, and six amino acids in H. sinensis reached the FAO/WHO standards. The taste activity value was highest for aspartic acid (13.0–14.5), followed by the glutamic acid. 5) The EPA, DHA, total monounsaturated fatty acid, and total polyunsaturated fatty acid contents were highest in H. hyotis. The DHA/EPA content was highest in H. inaequivalvis (2.081) and lowest in H. sinensis (1.590). The EPA+DHA content in the stone oysters was 17.47–32.78 mg/100 g. The atherogenicity index was the lowest and highest in H. hyotis and H. inaequivalvis, respectively; the thrombogenicity index for the three stone oysters was 0.037–0.068, which is considerably lower than that of scallop and fish. All three stone oyster species have high protein and low fat contents, and their adductor muscles provide superior marine animal proteins. The essential amino acid content in H. sinensis was more balanced, whereas H. hyotis had the most balanced fatty acids and health effects. However, all three species were high in saturated fatty acids, which contribute to thrombogenicity prevention. The composition and quality of the adductor muscles of stone oysters were studied. Our results provide a reference for the development and use of the Hyotissa germplasm on Weizhou Island.