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Summary Brown rice‐based foods are thought to be effective in preventing obesity. In this study, the effect of whole‐grain flat rice noodles (WFRN) on lipid metabolism as well as their relationship with gut microbiota was investigated in mice fed a high‐fat diet (HFD). The results indicated that WFRN reduced the degree of obesity, the lipid levels in the liver and serum, and the risk of liver inflammation. Moreover, WFRN significantly increased the contents of total short‐chain fatty acids (SCFAs) (from 162.06 ± 29.79 to 272.97 ± 59.26 μg mL−1; P < 0.05) and reshaped the composition of gut microbiota in mice cecum. As the beneficial bacteria with boosted abundance, higher Coriobacteriaceae_UCG‐002 was negatively related to the lipid levels in the liver and serum, and positively correlated with the content of hexanoic acid. On the contrary, the lower abundance of harmful bacteria Staphylococcus was positively correlated to body fat and inversely related to isovaleric acid, and Helicobacter was positively associated with higher serum LDL‐C and lower hexanoic acid. This study suggested that WFRN played a positive role in ameliorating lipid accumulation and inflammation caused by obesity, and this effect was closely associated with the regulation of gut microbiota and SCFAs.