The objective of this study was to investigate toxicity effects of ammonia nitrogen on the cuttlefish Sepia pharaonis. The effects of ammonia nitrogen stress (1, 3, 6, and 12 mg/L) on the blood cell immunity and liver antioxidant function were studied. The results showed that the number of blood cells, respiratory burst activities of blood cells, the phagocytosis rate of blood cells, Cu/Zn–superoxide dismutase (Cu/Zn–SOD) and catalase (CAT) activities and relative gene expression, and MDA content of the cuttlefish S. pharaonis were significantly affected by the ammonia nitrogen (P < 0.05). The number of apoptotic blood cells, respiratory burst activities of blood cells and contents of MDA were increase, phagocytosis of blood cells, SOD and CAT activity were decrease with long-term exposure to low concentration (1 mg/L) or high concentration (>3 mg/L) of ammonia nitrogen stress, and action degree is positively related to the stress of ammonia nitrogen concentration and time length treated. In summary, the ammonia nitrogen stress could result in declining phagocytic percentage, decreasing the activity of phagocytic, SOD and CAT, increasing the contents of MDA. It resulting in an imbalance of non-specific immune system and damaging antioxidant defense system, reducing the ability of eliminating free radicals, damaging cell membrane structure, then its functions of the cells and tissues of the body, which was a contributory cause of ammonia poisoning.