Previous studies have shown that trimethylamine N-oxide (TMAO), a gut microbiota-related metabolite, plays a significant role in the development and progression of cardiovascular disease (CVD). How to regulate the structure of gut microbiota to reduce circulating TMAO levels in the host is currently one of the hot topics in research. Diet is a major factor shaping the structure of gut microbiota. Through the exploration of dietary elements, we have found that multiple epidemiological studies suggest an inverse correlation between the intake of isoflavones and CVD, indicating that isoflavones are potential agents for the prevention and treatment of CVD. Interestingly, isoflavones have poor water solubility and low bioavailability. Several studies have confirmed interactions between isoflavones and gut microbiota, suggesting that the gut and gut microbiota are likely important therapeutic targets for isoflavones in preventing and treating CVD. Furthermore, a high-fat diet (HFD) is also an independent risk factor for CVD. Research literature indicates that HFD can disrupt both the gut and gut microbiota. As a biomarker for CVD risk, TMAO has been reported in some studies to increase in circulation following HFD intake, but the mechanisms behind this phenomenon require further exploration. Based on the above literature, we propose a scientific hypothesis: Can isoflavones regulate gut microbiota and subsequently reduce serum TMAO levels in HFD-fed mice? This hypothesis can be further divided into three specific scientific questions: Which isoflavones can reduce serum TMAO levels in HFD-fed mice? Is gut microbiota the key factor through which isoflavones reduce serum TMAO levels in HFD-fed mice? What mechanisms do these substances use to modulate gut microbiota?