Chinese mitten crab, a featured macrobenthos, has been one of the most important economical aquatic species in China. This study assessed the accumulation of an organochlorine pesticide methoxychlor (MXC) in Chinese mitten crab during exposure to 1 mg/L of MXC. The results showed the residual concentration of MXC in the ovary and hepatopancreas reached 55.07 ± 2.64 ng/g and 34.51 ± 2.35 ng/g, respectively. After exposure, tubular vacuolization of epithelial tissues, condensed egg cells and obvious intervals between egg cell wall and stroma were observed in the hepatopancreas and ovary, respectively. Significant changes of three key metabolic enzymes in hepatopancreas were observed upon exposure to MXC. Compared to the control, acetylcholinesterase level was significantly higher at day 7 (0.15 ± 0.01 vs. 0.06 ± 0.00 U/mgprot); glutathione S-transferase level was elevated at both day 4 (12.01 ± 0.48 vs. 3.20 ± 0.44 U/mgprot) and day 7 (12.84 ± 1.01 vs. 8.22 ± 0.81 U/mgprot); superoxide dismutase was sharply increased at day 4 (21.20 ± 0.24 vs. 3.66 ± 0.60 U/mgprot) but decreased at day 7 (3.74 ± 0.12 vs. 9.44 ± 0.85 U/mgprot). Overall, dissolved MXC accumulated in lipid-rich tissues could cause damages on epithelial cells and egg cells and change metabolic activities of enzymes involved in antioxidative stress and detoxification processes.