Desiccation is an important environmental stressor during crabs culture and transportation. In this study, we investigated oxidative damage, antioxidant capacity, immune-related enzyme activity and intestinal microbiota responses of Eriocheir sinensis subjected to aerial exposure stress for 96 h. The results revealed a significant increase in lipid peroxide (LPO) and malondialdehyde (MDA) levels in the hepatopancreas after aerial exposure (p < 0.05). Antioxidant activities including superoxide dismutase (SOD) and total antioxidant capacity (T-AOC) showed significant variations (p < 0.05). Alkaline phosphatase (AKP) and acid phosphatase (ACP) activity both increased to the maximum levels at 12 h, and were significantly lower than those of controls at 72 h and 96 h respectively (p < 0.05). High-throughput 16S ribosomal DNA (rDNA) sequencing revealed that aerial exposure stress altered bacterial diversity, and changed the composition of intestinal microbes. Specifically, abundance of beneficial bacteria Citrobacter decreased, while abundance of pathogenic bacteria Acinetobacter increased. The results revealed that prolonged period of air exposure stress adversely affects the antioxidant status, immune function, and intestinal flora in E. sinensis. This work could help to uncover the mechanisms of aerial exposure stress responses in this species.