Cryoprotectants are widely used to protect muscle tissue from ice crystal damage during the aquatic products freezing process, but traditional phosphate cryoprotectants may cause an imbalance in the calcium-to-phosphorus ratio for the human body. This study evaluated the effects of carrageenan oligosaccharides (CRGO) on quality deterioration and protein hydrolysis of crayfish (Procambarus clarkii) during superchilling. The physical-chemical analyses showed that CRGO treatments could significantly (p < 0.05) inhibit the increase of pH values, TVB-N, total viable counts, and thawing loss, and improve the water holding capacity and the proportion of immobilized water, which indicated that CRGO treatment effectively delayed the quality deterioration of crayfish. The myofibrillar protein structural results demonstrated that the increase of the disulfide bond, carbonyl content, S0-ANS, and the decrease of total sulfhydryl content were suppressed significantly (p < 0.05) in CRGO treatment groups. Furthermore, SDS-PAGE results showed that the band intensity of myosin heavy chain and actin in CRGO treatment groups were stronger than in the control. Overall, the application of CRGO to crayfish might maintain better quality and stable protein structure during the superchilling process, and CRGO has the potential to replace phosphate as a novel cryoprotectant for aquatic products.