Perchlorate is a well-known thyroid-disrupting chemical as well as an extremely stable inorganic pollutant widely distributed in the environment. Therefore, perchlorate posts potential risks to the environment as well as human health. Crayfish is a dominant aquatic food with increasing consumption levels in recent years. It is crucial to evaluate the accumulation of perchlorate with well-water-soluble properties in crayfish and to assess its health risks. In our present study, we obtained crayfish samples from cultivated ponds and markets based on the regions of the Middle and Lower Reaches of the Yangtze River. The perchlorate concentration was measured in all 206 samples using ultra-high performance liquid chromatography coupled with mass spectrometry (UPLC–MS). Monte Carlo simulation was used to perform health risk assessments. The results indicated that perchlorate levels ranged from 7.74–43.71 μg/kg for cultivated crayfish and 4.90–16.73 μg/kg for crayfish sold in markets. The perchlorate accumulation mainly occurred in exoskeleton parts. All the HQ values were remarkable, at less than one—indicating that perchlorate exposure through the ingestion of crayfish does not pose an appreciable risk to human health.