As an important aquaculture shellfish, the superior taste and high nutritional value of oyster (Crassostrea gigas Thunberg) have drawn extensive attention. In this study, twenty-one free amino acids (FAAs) and six 5′-nucleotides were evaluated through stable isotope labeling-liquid chromatography coupled with tandem mass spectrometry (SIL-LC-MS/MS), and the lipid profile was explored using ultrahigh performance liquid chromatography-Q Exactive HF mass spectrometry (UHPLC-QE/MS). The adductor muscle of the oyster possessed a high level of sweetness-related amino acids (Arg, Gly and Hyp) and 5′-nucleotides. A total of 149 lipid species were detected in different tissues of oysters, including 17 triacylglycerols (TAGs), 6 diacylglycerols (DAGs), 61 phosphatidylcholines (PCs), 29 phosphatidylethanolamines (PEs), 11 lysophosphatidylcholines (LPCs), 8 lysophosphatidylethanolamines (LPEs), and 1 lysophosphatidylinositol (LPI). FAAs, 5′-nucleotides and lipid profile in the digestive gland of oysters can be divided into three stages, from November to April, May to July, and August to October. The highest proportion of umami-taste amino acids and 5′-nucleotides appeared from March to May. The highest percentage of high unsaturation degree glyceride and phospholipids appeared in August and April, respectively. Thus, the results reported in this study are important for product development and sustainable exploitation in the future.