In order to detect the pathologic changes of tissue structure in clams (Ruditapes philippinarum), the hematoxylineosin stain (H－E) method was employed after 20 days of exposure to hypoxia (DO <2 mg·L^-1) stress. Oxygen consumption, ammonia excretion rate, CO₂ production and O:N ratio was also measured in clams exposed to hypoxia on the 2nd, 5th, 10th and 20th day. The results showed that a visible structural difference was observed between the hypoxia and control groups. Scattered deeppurple round spots distributed in the clam tissues of the hypoxia group, which might be due to abnormal lipid metabolism to form the lipid accumulation in the clams exposed to hypoxia. At 22 ^oC water temperature, oxygen consumption, ammonia excretion rate and CO₂ production of clams were significantly affected by hypoxia stress. The rates of oxygen consumption, ammonia excretion and CO_2 production of the clams decreased when exposed to hypoxia on the 2nd day, with their values being 0.566 mg·g^-1·h^-1, 0.079 mg·g^-1·h^-1 and 26.236 mg·g^-1·h^-1 respectively. The oxygen consumption and ammonia excretion rates reached the lowest level on the 2nd day. But the CO₂ production rate reached the lowest value (7.422 mg·g^-1·h^-1) on the 20th day, which was about one half compared to the control group. The O:N ratio was 6.25-12.11 in the hypoxia group, and it reached the maximum value of 12.11 on the 20th day. Therefore, hypoxia had an important impact on the tissue structure and physiological metabolism in clams. The results could provide a theoretical basis for the scientific management of clam’s aquaculture.