To investigate the effect of Rosa roxburghii Tratt fruit vinegar (RFV) on the intervention of obesity and hyperlipidemia and its potential mechanism, a high-fat diet (HFD)-induced obesity model in mice was established and gavaged with RFV, saline and xuezhikang for 30 consecutive days, respectively. The results showed that RFV supplementation significantly reduced fat accumulation, and improved dyslipidemia and liver inflammation in HFD mice. RFV intervention for 30 days significantly improved the diversity of gut microbiota and altered the structure of gut microbiota in HFD mice. Compared with the model group (MC), the ratio of Firmicutes to Bacteroidetes at least decreased by 15.75% after RFV treatment, and increased the relative abundance of beneficial bacteria (Proteobacteria, Bacteroidetes, Lactobacillaceae, Bacteroides, Akkermansia,) and decreased the relative abundance of harmful bacteria (Ruminococcaceae, Erysipelotrichaceae, Ruminococcaceae _UCG-013, Lachnospiraceae, Allobaculum, Actinobacteria). Spearman’s correlation analysis revealed that Erysipelotrichaceae, Allobaculum, Lachnospiraceae, Ruminococcaceae, Ruminococcaceae_UCG-013, uncultured_bacterium_f_Lachnospiraceae and Desulfobacterota were positively correlated (p < 0.05) with the body weight of mice, while Proteobacteria was negatively correlated (p < 0.05) with the body weight of mice. The two main bacteria that could promote dyslipidemia in obese mice were Actinobacteria and Firmicutes, while those that played a mitigating role were mainly Bacteroidetes. It is concluded that RFV plays an important role in the intervention of obesity and related complications in HFD mice by regulating their gut microbiota.