Background: Whole grains present distinguished benefits to a handful of metabolic syndromes (MetS). However, the preventive effects of germinated brown rice (GBR), a new type of brown rice, on patients with type 2 diabetes (T2DM) are rarely reported. Objectives: To investigate whether replacing 100 g refined white rice (RWR) with equal GBR per day is effective in T2DM and its underlying mechanisms. Methods: Ninety-nine qualified T2DM patients (64.58 ± 5.06 years old) were recruited. All patients were randomly divided into GBR group (100 g d^-1 GBR for 12 weeks) and control group (keep the regular diet). Food frequency questionnaires, and fresh stool and serum samples were collected before and after the intervention, followed by various measurements. Results: Fasting blood glucose was obviously decreased after GBR intervention with an effective rate of 62%. Glycated hemoglobin (HbA1c) levels were decreased in the GBR group with no significance. In the GBR group, the abundance of beneficial bacteria in feces was increased, while harmful bacteria were decreased. The percentage of Bacteroides (57.2%) was largely increased. In addition, three types of short-chain fatty acids (SCFAs) including acetic acid, propanoic acid, and butyric acid were increased significantly by GBR (p < 0.05). The secretion of GLP and PYY in serum, two kinds of gastrointestinal hormones downstream of SCFAs, was stimulated by GBR (p < 0.01). Meanwhile, GBR intervention could balance the ratio of Treg/Th17 immune cells in PBMCs and reduce the levels of inflammatory factors including IL-6, IL-8, and LPS in serum, which improved the permeability of intestinal mucosa. Conclusions: GBR (100 g d^-1 for 12 weeks) has positive improvement in the fasting blood glucose for T2DM patients, which attributed to the recovery of intestinal homeostasis.

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