<p>Ammonia-N represents the most toxic nitrogen compound for crustaceans. Melatonin (MT), a natural antioxidant, is capable of efficiently mitigating oxidative damage within the body. The objective of this experiment was to evaluate the protective effect of melatonin pretreatment on the Chinese mitten crab (<i>Eriocheir sinensis</i>) under ammonia-N stress and to analyze the potential connection between the protective effect of MT and the intestine–hepatopancreas axis. A 14-day feeding trial and a 48-h acute ammonia-N stress trial were employed to explore the influence of MT feeding on the antioxidant capacity, immunity, and gut microbiota of the Chinese mitten crab. The findings demonstrated that acute ammonia-N stress disrupted the histoarchitecture of the crab’s hepatopancreas and diminished the antioxidant and nonspecific immunity of the crab. When exposed to ammonia-N subsequent to MT pretreatment, the activities of Superoxide dismutase (SOD), catalase (CAT), total antioxidant capacity (T-AOC), and glutathione peroxidase (GSH-Px) were significantly up-regulated in the hemolymph of crabs (<i>P</i> &lt; 0.05), while the malondialdehyde (MDA) level was significantly down-regulated (<i>P</i> &lt; 0.05). Moreover, in the hepatopancreas, the activities of GSH-Px and CAT were significantly up-regulated (<i>P</i> &lt; 0.05), while lysozyme (LZM) activity was significantly down-regulated (<i>P</i> &lt; 0.05). In the hemolymph, the activities of acid phosphatase (ACP) and alkaline phosphatase (AKP), along with the levels of total protein (TP) and albumin (ALB), were significantly increased (<i>P</i> &lt; 0.05). The results indicate that MT pretreatment can safeguard against acute ammonia-N stress, enhancing the antioxidant capacity and innate immunity of the hepatopancreas and hemolymph in the crab. Additionally, ammonia-N stress induced an imbalance in the gut flora and reduced the abundance and diversity of the gut flora. Conversely, the Shannon index of the α-diversity of the gut flora of the Chinese mitten crab was elevated following MT feeding. Therefore, acute ammonia-N exposure inflicted significant oxidative damage and immune function impairment in the hemolymph and hepatopancreas of crabs. However, pretreatment with MT protected the organism and substantially alleviated the damage caused by ammonia-N exposure. Furthermore, these results suggested a close association between the intestine and the hepatopancreas in crabs. Correlation analyses also confirmed that the protective effects of MT might be contingent upon the intestine–hepatopancreas axis.</p>