The study of the fungal communities of the skin constitutes a pivotal component of skin microbiome research. Within these communities, the genus Malassezia stands out as a major constituent, representing 50% to 80% of the total fungal colonization on the skin of healthy individuals. The excessive growth or metabolic irregularities of this genus are intimately connected with the onset of various skin disorders that are intrinsically linked to its lipid-dependent nature. Cutaneous lipid metabolism is indispensable for maintaining the skin barrier function and skin health. Malassezia possesses the ability to encode multiple lipase genes, and the secretion of these lipases plays a pivotal role in the survival strategies of the fungi. This review explores recent advances in the ecological niche of Malassezia in skin microecological homeostasis, its mechanism of disrupting skin lipids through catabolic metabolites, and the relationship between this disruption of the skin lipid barrier and skin diseases. This review offers a reference for future research on the mechanisms by which Malassezia affects lipid metabolism and provides a theoretical foundation for the development of innovative therapeutic approaches for dermatological conditions.