The razor clam Sinonovacula constricta is a commercial benthic bivalve, and burrows the deeper cave than the other buried benthic bivalves. Due to the little exchange of seawater and to anoxic conditions, S. constricta is exposed to considerable amounts of sulfide during low tide, but exhibits strong sulfide tolerance. Mitochondrial sulfide oxidation is a particular defense strategy against sulfide toxicity of sulfide-tolerant organisms, for which sulfide:quinone oxidoreductase (SQR) is the first key enzyme. In order to investigate the mechanism of sulfide tolerance in S. constricta, its SQR (designated as ScSQR), was cloned and characterized. The full-length cDNA of ScSQR was 3698 bp and encoded 443 amino acids. The deduced ScSQR protein contained conserved FAD-binding domains, two cysteine residues, two histidines, and one glutamic acid, which are the essential elements for the catalytic mechanism of SQR. Subcellular localization analysis by the TargetP 1.1 prediction and the Western blot confirmed that ScSQR was only located in the mitochondria. The response of ScSQR in the gill and liver of S. constricta were investigated during sulfide exposure (50, 150, and 300 μM sulfide) for 0, 3, 6, 12, 24, 48, 72, and 96 h by qRT-PCR. Moreover, the time-course expressions of ScSQR protein in the S. constricta gill were detected when exposed to 150 μM sulfide by Western blot. The expression level of ScSQR increased significantly and showed a time-dependent pattern. In addition, under sulfide stress, the expression level of the gill was higher than that of liver. Together, our results suggest that ScSQR may perform important roles in protecting cells from sulfide stress by participating in mitochondrial sulfide detoxification and providing high sulfide tolerance to S. constricta.