The dissolved oxygen (DO) concentration that induces the onset of anaerobic metabolism in hard clams was found to be 1.11 mg O2 L−1, at which time, the concentration of succinate in the body fluid was 4.4 μmol mL−1. When the DO concentration was <1.11 mg O2 L−1, the burial depth was significantly reduced, and succinate significantly accumulated in the body fluid. After 24 h of anoxic exposure, succinate had accumulated in the gills and equal amounts of succinate and alanine had accumulated in the foot. This indicates that carbohydrates in the gills and amino acids in the foot contribute to anaerobic energy production. The accumulation rates of succinate and propionate in the body fluid were the highest compared with those in other tissues, while no accumulation of alanine in the body fluid was found. The recovery rates of succinate in the body fluid and alanine in the foot were the highest compared with those in other tissues. The results of this study suggest that the DO concentration in the bottom water of clam ponds should be maintained at ≥1.11 mg O2 L−1, and the anoxia-tolerant ability of hard clams can be assessed by the contents of carbohydrates.