Obesity, often caused by disorders of lipid metabolism, is a global health concern. Flavonoids from staple grains and legumes are expected as a safer and more cost-effective alternative for the future development of dietary flavonoid-based anti-obesity dietary supplements or drugs. This review systematically summarized their content variation, metabolism in the human body, effects and molecular mechanisms on lipid metabolism. These flavonoids intervene in lipid metabolism by inhibiting lipogenesis, promoting lipolysis, enhancing energy metabolism, reducing appetite, suppressing inflammation, enhancing insulin sensitivity, and improving the composition of the gut microbial. Fermentation and sprouting techniques enhance flavonoid content and these beneficial effects. The multidirectional intervention of lipid metabolism is mainly through regulating AMPK signaling pathway. This study provides potential improvement for challenges of application, including addressing high extraction costs and improving bioavailability, ensuring safety, filling clinical study gaps, and investigating potential synergistic effects between flavonoids in grains and legumes, and other components.