The stressful effect of Cu²⁺ with exposure duration for 96 hours on physiology metabolism, histopathological structure and enzyme activity of ark shell Scapharca broughtonii was studied by the methods of biological toxicity test. The incubating concentrations of Cu²⁺ were set at (0.01, 0.05, 0.10, 0.50, 1.00) mg/L and a control group was set with no Cu²⁺ stress (normal seawater). Results showed that incubating concentration and exposure duration both had significant influence on physiological indices of S. broughtonii, including oxygen consumption rates (OR), ammonia excretion rates (NR) and ratios of O to N (O∶N). The OR, NR and O∶N all decreased sharply after initial exposure to the Cu²⁺ stress. The minimum values for OR, NR and O∶N were found to be (0.005±0.001) mg/(g·h), (0.5±0.05) μmol/(g·h), 0.7±0.1 with the 1.00 mg/L treatment at the end of the experiment, which equaled 1%, 29%, 3% of control groups, respectively. Generally, apparently reduced metabolic rate of S. broughtonii individuals exposed to Cu²⁺ stress was observed within 72 h. After 72 h, each group with different Cu²⁺ concentration behaves differently. After being incubated at 0.01 mg/L for 96 h, the S. broughtonii seemed to be acclimated to Cu²⁺ stress. Metabolic rates of the animals were restored to the control level, while O∶N was not different from the control groups and no detectable histopathologic damage was found. The physiological metabolism and histopathological structure of individuals under concentrations that higher than 0.05 mg/L Cu²⁺ were significantly affected after 96 h, while most of the O∶N in all the experimental groups were below 9 and histopathologic damage such as gills damage and tissues messy structure were found. The ACP and ALP activities of individuals exposed to 0.10 mg/L Cu²⁺ increased in gill and decreased in hepatopancreas, while GPX and GST increased in both tissues. Our results demonstrated that incubating concentration (≥0.05 mg/L) after 96 h exposure significantly affect physiological metabolism and histopathological structure of the ark shell. ACP, ALP, GPX and GST activities of individuals incubated at 0.10 mg/L were significantly affected. Our results provide the basic data for studying the response mechanism of S. broughtonii and other coastal shellfishes to Cu²⁺ stress, and referential data for the prevention and biological reparation of potential heavy metal pollution risk in coast area.