The invention discloses a Kluyveromyces marxianus C2 and a preparation method and an application thereof. The preservation number of the Kluyveromyces marxianus C2 is CCTCC NO: M2014059. The aflatoxin B1, zearalenone and ochratoxin A can be degraded by Kluyveromyces marxianus C2 and the biodegradation rate reaches more than 80%. The fermented Kluyveromyces marxianus C2 is put into toxin-contaminated liquid or solid food or feed matrix at a certain ratio to enable mycotoxins to be fast, safely and efficiently degraded and detoxified and can also be used for oral detoxification of animals. The strain disclosed by the invention has the advantages of low production cost and safe application and has wide application prospects.