Monascus-fermented cheese (MC) is a new cheese product that undergoes a multistrain fermentation process, which results in unique flavor qualities. Lipid metabolism plays an important role in the flavor formation of MC. To clarify the lipid composition of MC and the changes in lipid composition at four ripening periods, this study resolved the lipid profiles of MC by using UHPLC-QTRAP MS. The results identified 21 lipid classes and 748 lipid species, 72 of which were significantly different (VIP > 1, p < 0.01, |log 2FC| > 1). Additionally, 83 relevant metabolic pathways were enriched. Based on the enriched metabolic pathways and lipid changes, the pathways of differential lipid formation in MC were mapped. The results of this study comprehensively characterize the changes in lipids during the ripening process of MC, which can be used in the future to deeply analyze the mechanism of flavor formation in MC.