Patulin is one of the mycotoxins that exists in abundance in fruits and derivative products and is easily exposed in daily life, leading to various toxicities such as genotoxicity, teratogenicity, immunotoxicity, and carcinogenicity in the human body, while the efficient removal or degradation measures are still in urgent demand. In this work, Saccharomyces cerevisiae, a natural yeast with both patulin degradation and intestine damage protection abilities, was first applied to prevent and decrease the hazard after patulin intake. In vitro, Saccharomyces cerevisiae KD (S. cerevisiae KD) could efficiently degrade patulin at high concentrations. In a Canenorhabditis elegans (C. elegans) model fed on S. cerevisiae KD, locomotion, oxidative stress, patulin residual, intestine damage, and gene expression were investigated after exposure to 50 μg mL-1 patulin. The results demonstrated that S. cerevisiae KD could efficiently degrade patulin, as well as weaken the oxidative stress and intestinal damage caused by patulin. Moreover, S. cerevisiae KD could regulate the gene expression levels of daf-2 and daf-16 through the IGF-1 signaling pathway to control the ROS level and glutathione (GSH) content, thus decreasing intestinal damage. In summary, this work uncovers the outstanding characteristic of an edible probiotic S. cerevisiae KD in patulin degradation and biotoxicity alleviation and provides enlightenment toward solving the hazards caused by the accumulation of patulin.