This study aimed to evaluate the effects of different liquid nitrogen freezing (LNF) temperatures (-20, -40, -60, -80, and -100 °C) on the water holding capacity, texture, microstructure, and flavor of Crassostrea gigas (C. gigas). The results showed that -40 °C LNF, -60 °C LNF, and -80 °C LNF improved the water holding capacity of C. gigas (P < 0.05); -60 °C LNF and -80 °C LNF could effectively maintain the hardness of the body trunk and adductor muscles. Compared with -20 °C refrigerator freezing (RF), the LNF group could form smaller ice crystals and thus reduce the damage to the muscle cell structure damage, especially LNF at -80 °C. Gas chromatography-ion mobility spectrometry (GC-IMS) and e-nose results indicated that -80 °C LNF maintained the flavor profile of few aldehydes and alcohols compared to other freezing groups. Therefore, -80 °C LNF effectively improved the quality and maintain the flavor characteristics of frozen C. gigas.