The Pacific oyster (Crassostrea gigas) is one of the most important aquaculture species worldwide. Its meat quality is vital for consumer satisfaction, and nutrient content, especially glycogen, is closely associated with oyster fatness and meat colour. Fluctuations in nutrient content of short‐term starvation have not been previously reported, and seasonal variation in glycogen content in different tissues has rarely been reported. In the present study, we investigated these important aspects of oyster production and found that short‐term starvation (50 hr) did not significantly alter glycogen, protein or lipid content. The seasonal variation assay showed that glycogen and lipid accumulation was high in autumn and winter and that seawater temperature and protein content were inversely related to glycogen content. Glycogen content of the whole flesh was higher from January to April and was positively related to the condition index before the onset of gametogenesis. Glycogen content was higher in the gonad, labial palp and mantle compared to the gill or adductor muscle. Relative expression of genes encoding proteins involved in glycogen metabolism (glycogen synthase, glycogen phosphorylase, glycogen debranching enzyme and glycogen branching enzyme) was closely associated with the glycogen content in the corresponding tissues. Glycogen content in the gonad was regulated by glycogen metabolic and glycolysis pathway genes (6‐phosphofructo kinase, phosphoglycerate kinase, pyruvate kinase, hexokinase and glucose transporters), and stored glycogen was the main energy source for gametogenesis. These findings contribute to oyster aquaculture management and glycogen improvement and expand our understanding of glycogen metabolism in oysters.