Patulin, a polyketide secondary metabolite produced by fungi, is a major mycotoxin in fruits and their processed products. Penicillium expansum is the primary agent for patulin contamination in food. P. expansum infects most bulk and special fruits, causes serious postharvest decay, and simultaneously produce patulin. The circulation and processing of fresh fruits can introduce patulin into the food chain, which pose a potential threat to the health of consumers. Patulin may damage vital organs in both humans and animals and causes acute and chronic symptoms. The food safety issues caused by patulin contamination are attracting increasing attention, and patulin-related research has become a hot topic. The research advances in patulin biosynthesis and regulation mechanisms were comprehensively summarized. The gene cluster of patulin biosynthesis, catalytic enzymes in different steps of the biosynthetic pathway, and the molecular pathway of patulin biosynthesis and intermediate product transport were introduced. The complex regulatory network of patulin biosynthesis from the aspects of specific regulatory factor of biosynthetic pathway, global regulatory factors responding to environmental signals such as light, pH value, carbon source, and sulfur source, as well as epigenetic factors involved in histone methylation and acetylation modifications were described. The source control and removal strategies for patulin contamination in food were elaborated. The main control technologies based on physical, chemical, and biological principles were summarized, respectively, and the advantages and disadvantages of different control strategies were raised. Finally, the relationship between the research of patulin biosynthetic mechanisms and the development of contamination control technologies was discussed. The green and safe biological control methods as the promising technology was emphasized.