Perchlorate is a ubiquitous environmental contaminant worldwide, recognized as an emerging thyroid toxicant. This study focused on the pollution status, spatial distribution, possible sources of perchlorate in raw cow milk collected from 155 dairy farms in China, as well as the health risk of exposure to perchlorate through dairy products. The results showed that the detection rate of perchlorate in raw milk was 100% with the mean of 15.9 μg/kg, indicating the ubiquitous contamination of perchlorate in raw milk from China. The simulation of spatial distributions indicated that the levels of perchlorate in raw milk were spatially correlated, and relatively high levels of perchlorate exist in certain parts of Beijing-Tianjin-Hebei, Shanxi, Henan, and Zhejiang, suggesting potential environmental perchlorate contamination in these regions. A positive correlation was found between the perchlorate level in milk and the perchlorate level in feed, indicating the transfer process of perchlorate from feed to milk. The hazard quotient (HQ) values of exposure to perchlorate by dairy products ranged between 0 and 2.14, with the mean of 0.0188 and P95 of 0.101, indicating relatively low health risk to perchlorate through dairy products. To our knowledge, this is the first nationwide study on the spatial distribution and risk assessment of perchlorate in raw cow milk from China.