The safety of the rice-fish co-culture system (RFCS) is threatened by severe soil cadmium (Cd) pollution. However, the characteristics of Cd accumulation in aquatic animals within this system remain poorly understood. To investigate the Cd accumulation characteristics and dietary risks in aquatic animals with varying habitat characteristics, three species — crayfish Procambarus clarkii, loach Paramisgumus dabryanus, and crucian carp Carassius auratus — were cultured in RFCS with soil Cd pollution ranging from 0.2 to 32.0 mg/kg. The results demonstrated that the survival of the three aquatic animals did not differ significantly at medium to low Cd concentrations (0.2–4 mg/kg) but decreased markedly at high concentrations (16–32 mg/kg). The WGR of crayfish decreased as the Cd treatment concentration increased. The Cd accumulation in various tissues showed an increasing trend with increasing Cd exposure. At the same concentration, the accumulation of Cd was in the order of liver (or hepatopancreas) ≈ intestine > gill > muscle. At the same Cd treatment concentration, the Cd accumulation in different animal species generally showed a trend of crayfish > loach > crucian carp, indicating that accumulation of Cd in the aquatic animals within the Cd-contaminated RFCS is closely related to their habitat characteristics. The soil pollution thresholds for crayfish, loach and crucian carp were determined to be 11.7, 38.8 and 90.5 mg/kg, respectively, which can serve as early warnings for safe production. Within the tested concentration range, the aquatic animals did not pose non-carcinogenic risks; however, they posed carcinogenic risks when these animals are exposed to high soil Cd concentrations.