The Chinese mitten crab (Eriocheir sinensis), as a benthic animal, adequate oxygen is very important for their life activities. This study was designed to evaluate the damage of the gill structure and function of E. sinensis under acute hypoxia (DO = 0.5 mgO2L−1,4 h) and the anti-injury effects of melatonin (MT). Histological examination showed predominantly regressive changes in the gills of crab exposed to hypoxia. The histoarchitecture of gills in the hypoxia group showed disrupted pillar cells (PC), the accumulation of hemocytes (HeM) in the hemocoelic space, lifting of lamellar epithelium and the appearance of bigger size of distal tips. Whereas, no such changes were found in MT group. Compared with the Control+hypoxia (C_hyp) group, the MDA of MT + hypoxia (MT_hyp) was significantly decreased (p < 0.05), while the Na+-K+ATPase content obviously increased in MT_hyp (p < 0.05). Hypoxia promoted the CAT and GSH-PX activities in gills, meanwhile, SOD, CAT and GSH-PX activities significantly increased in MT_hyp group after 4 h of hypoxia compared to Control+normoxia (C_nor) group (p < 0.05). Next, we observed the changes of oxygen consumption rate (OC) and the number times of opening-and-closing water inlet (OCWI) in each group within 1 h after reoxygenation. We found that both MT + normoxia (MT_nor) and MT_hyp groups in oxygen consumption rate after reoxygenation obviously higher than that of C_hyp and C_nor group at 2 mins. The number times of OCWI in C_hyp and MT_hyp groups were significantly higher than that of C_nor and MT_nor groups (p < 0.05) after reoxygenation for 2 mins. In summary, the number times of OCWI be used as an index to evaluate hypoxia for E. sinensis. MT is demonstrated as an antioxidant not only related to the antioxidant ability, but also to the protective gill structure and regulation respiratory for E. sinensis.