Climate change has been considered as a main threat for food safety by influencing on crop production and food supply chain through the change in temperature and humidity. To prevent risks of mycotoxins from climate change, it is important to predict mycotoxin risks with statistical approaches and stepwise process to compile large volume of datasets, such as climate change, contamination level, and cultivation area in specific regions. This paper aims at prioritization of vulnerable mycotoxins related to climate change in Korea. In addition, this paper focuses on prioritization of vulnerable raw materials for specific mycotoxins and prediction of vulnerable regions for vulnerable raw materials in Korea. Among six target mycotoxins (deoxynivalenol, fumonisin (B1 and B2), ochratoxin A, patulin, total aflatoxin (B1, B2, G1, and G2), and zearalenone), ochratoxin A (OTA) and total aflatoxin (TA) were identified as specific vulnerable mycotoxins. In addition, 4 raw materials (chestnut, dried red pepper, perilla seed, and soy bean) were identified as vulnerable raw materials for OTA and TA and vulnerable regions were predicted to be moved to the northward areas in Korea. These results can be utilized to design long-term national sampling plan for mycotoxins in food considering climate change in Korea.