The hepatopancreas of swimming crab (Portunus trituberculatus) rich in carotenoids would undergo serious color deterioration during cold storage, and then made portunid lose its commodity value. In this study, we firstly elucidated the change mechanism of its carotenoids during storage at the molecular level using transcriptome technology. We concluded that low-temperature would inhibit aerobic respiration of portunid, leading to a lower pH and inducing the degradation of carotenoids. After that, longer cold storage time would increase the oxidative stress in portunid, resulting in a further decrease in carotenoids content. Finally, the strong autolysis of portunid could release carotenoids stored in other parts such as ovary to the external environment, resulting in the increase of carotenoids detection content. This research could provide a basis for further developing the fresh-keeping technology of portunid during low-temperature storage.