Crabs can live in diverse lifestyles in both water and benthic environments, which are the basin of microplastics (MPs) inputs. Edible crabs with large consuming quantity, e.g., Scylla serrata were subjected to accumulate MPs in their tissues from surrounding environments and generate biological damages. However, no related research has been conducted. In order to accurately assess the potential risks to both crabs and humans consuming MPs contaminated crabs, S. serrata were exposed to different concentrations (2, 200 and 20,000 μg/L) of polyethylene (PE) microbeads (10–45 μm) for 3 days. The physiological conditions of crabs and a series of biological responses, including DNA damage, antioxidant enzymes activities and their corresponding gene expressions in functional tissues (gills and hepatopancreas) were investigated. PE-MPs accumulated in all tissues of crabs with concentration- and tissue-dependent manner, which was assumed to be via the internal distribution initialized by gills’ respiration, filtration and transportation. Significantly increased DNA damages were observed in both gills and hepatopancreas under exposures, however, the physiological conditions of crabs showed no dramatic alterations. Under low and middle concentration exposures, gills energetically activated the first line of antioxidant defense to against oxidative stress, e.g., superoxide dismutase (SOD) and catalase (CAT), but lipid peroxidation damage still occurred under high concentration exposure. In comparison, SOD and CAT composed antioxidant defense in hepatopancreas tended to collapse under severe MPs exposure and the defense mechanism attempted to switch to the secondary antioxidant response by compensatively stimulating the activities of glutathione S-transferase (GST), glutathione peroxidase (GPx) and the content of glutathione (GSH). The diverse antioxidant strategies in gills and hepatopancreas were proposed to be closely related to the accumulation capacity of tissues. The results confirmed the relation between PE-MPs exposure and antioxidant defense in S. serrata, and will help to clarify the biological toxicity and corresponding ecological risks.