Socioeconomic advancement has led to a shift in dietary habits from monotonous to increasingly diverse patterns, placing a growing burden on the intestinal system. As a result, the number of patients with chronic inflammatory bowel disease (IBD) has continued to rise. IBD is an inflammatory condition with a complex etiology, and its onset and progression are closely linked to metabolic reprogramming. Among these, lipid metabolism disorders have been shown to play a critical role in IBD pathogenesis, compromising intestinal barrier function and driving inflammatory responses by modulating immune cell activation, cytokine release, and oxidative stress. In recent years, plant-derived flavonoids have garnered widespread attention for their abundance in foods and potent anti-inflammatory, antioxidant, and metabolic-regulatory properties. Emerging evidence suggests that plant-derived flavonoids can influence the progression of IBD by modulating lipid metabolism regulators, improving fatty acid metabolic pathways, and maintaining cholesterol homeostasis. However, the precise mechanisms through which plant-derived flavonoids exert their effects on IBD via lipid metabolic reprogramming remain to be fully elucidated. This review summarizes the mechanistic roles of lipid metabolic reprogramming in the pathogenesis of IBD, explores the potential of plant-derived flavonoids to modulate lipid metabolism, and discusses their possible mechanisms for alleviating IBD through metabolic regulation. These insights aim to provide new perspectives and scientific evidence to inform the development of dietary interventions for the prevention and management of IBD.