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Glycogen, a stored form of glucose, is an important form of energy for aquatic shellfish, contributing to the flavor and quality of the oyster. The glycogen synthase (GYS) and glycogen synthase kinase 3β (GSK3β) are two major enzymes in the glycogenesis. However, the information of the two genes in the Jinjiang oyster <i>Crassostrea ariakensis</i> remains limited. In this study, we identified the genes of <i>GYS</i> and <i>GSK3β</i> and further explored their function in the glycogen synthesis of <i>C. ariakensis</i>. The <i>GYS</i> and <i>GSK3β</i> were distributed in all tested tissues, and high expression of <i>GYS</i> and glycogen content were detected in the gonad, labial palp, hepatopancreas, and mantle, while the high expression of <i>GSK3β</i> was observed in the gill and adductor muscle. The expression of <i>GYS</i> was positively correlated with the glycogen content, while <i>GSK3β</i> was negatively correlated. Additionally, knockdown of <i>GSK3β</i> using RNAi decreased the <i>GYS</i> expression, revealing the negative regulatory effect of <i>GSK3β</i> on <i>GYS</i>. These findings enrich the research data of <i>GSK3β</i> and <i>GYS</i> involved in glycogen synthesis, providing valuable information for further research on the function of GSK3β and GYS in the glycogen synthesis process of oyster.