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This study investigated the hypolipidemic effect of whole grain Qingke (WGQ) and its influence on intestinal microbiota. Changes in the serum lipid, intestinal environment, and microbiota of Sprague-Dawley rats fed high-fat diets supplemented with different doses of WGQ were determined. Results showed that high doses of WGQ significantly decreased (P < 0.05) the Lee's index, serum total cholesterol, low-density lipoprotein cholesterol, and non-high-density lipoprotein cholesterol levels whereas they increased the body weight of the rats. Cecal weight and short-chain fatty acid (SCFA) concentration increased with increasing WGQ dose. An Illumina-based sequencing approach showed that the relative abundance of putative SCFA-producing bacteria Prevotella and Anaerovibrio increased in the rats fed the WGQ diet. Principal component analysis revealed a significant difference in intestinal microbiota composition after the administration of the WGQ diet. These findings provide insights into the contribution of the intestinal microbiota to the hypolipidemic effect of WGQ.