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Patulin-producing fungi pose an unavoidable problem for apple and its product quality, thereby threatening human and/or animal health. Studies on controlling the patulin-producing fungal growth and patulin contamination in apple and its products by physical methods, chemical fungicides, and biological methods have been performed for decades, but patulin contamination has not been addressed. Here, the important of studying regulation mechanism of patulin production in apple at the protein expression and metabolism levels is proposed, which will facilitate the development of controlling patulin production by using physical, chemical, and biological methods. Furthermore, the advantages or disadvantages and effects or mechanisms of using physical, chemical, biological methods to control the decay caused by Penicillium expansum and to remove patulin in food was discussed. The development of physical methods to remove patulin depends on the development of special equipment. Chemical methods are economical and efficient, if we have ensured that there are no unknown reactions or toxic by-products by using these chemicals. The biological method not only effectively controls the decay caused by Penicillium espansum, but also removes the toxins that already exist in the food. Degradation of patulin by microorganisms or biodegradation enzymes is an efficient and promising method to remove patulin in food if the microorganisms used and the degradation products are completely non-toxic.