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Cereals are one of the most important foods on which human beings rely to sustain basic life activities and are closely related to human health. This study investigated the effects of different steamed buns on intestinal microbiota. Three steamed buns were prepared using refined flour (RF), 1:1 mixed flour (MF), and whole wheat flour (WF). In vitro digestion simulations were conducted using a bionic gastrointestinal reactor (BGR) to examine their influence on intestinal microbiota. The results showed that at 0.5% addition, butyric acid and short-chain fatty acids in WF were significantly different from those in RF and MF (<i>p</i> < 0.05). WF also promoted the proliferation of beneficial microbiota, such as <i>Megamonas</i> and <i>Subdoligranulum</i>. At 0.5%, 1.0%, and 1.5% additions of WF, acetic acid and short-chain fatty acids at 1.5% WF increased by 1167.5% and 11.4% from 0.5% WF, respectively, and by 20.2% and 7.6% from 1.0% WF, respectively. WF also promoted the proliferation of <i>Bifidobacterium</i>, <i>Lactobacillus</i>, and <i>Bacteroides</i> and inhibited the growth of pathogenic microbiota, such as <i>Streptococcus</i>, <i>Enterococcus</i>, and <i>Klebsiella</i>. These findings support the consumption of whole cereals and offer insights into the development of new functional foods derived from wheat.