Ochratoxin A (OTA) is an important mycotoxin detected in edible oil, and it can be effectively removed by classical edible oil refining processes. However, the fate of OTA in the refining process has not been reported. In this study, we systematically tracked the OTA changes during the oil refining process by fortifying 100 μg/kg OTA in crude rapeseed oil. Results showed that about 10.57%, 88.85%, and 0.58% of OTA were removed during the degumming, deacidification, and decolorization processes. Among them, 16.25% OTA was transferred to the byproducts, including 9.85% in degumming wastewater, 5.68% in soap stock, 0.14% in deacidification wastewater, and 0.58% in the decolorizer; 83.75% OTA was found to transform into the lactone ring opened OTA (OP-OTA) during the deacidification stage, which is attributed to the hydrolysis of the lactone ring of OTA in the alkali refining. The OP-OTA was verified to distribute in the soap stock, and small amounts of OP-OTA could be transferred to deacidified wastewater when the OTA pollution level reached 500 μg/kg in crude rapeseed oil. The OP-OTA exhibited strong toxicity, especially nephrotoxicity, as reflected by the cell viability assay and in silico toxicity. Therefore, the safety of the soap stock processing products from OTA-contaminated rapeseed deserves attention.