Germinated brown rice (GBR) consists of bioactive compounds (BCs) that are very useful for diabetes treatment. Modified GBR-based flour (MGBRF) was produced by modifying the starch in GBR with 0, 299.19, 598.38, and 897.57 U/ml of cyclodextrin glycosyltransferase (CGTase) for 1 hr and then spray-dried to examine its antidiabetic and cytotoxic effects. The results showed that the slowly digestible starch and resistant starch by modifying the starch in GBR with 598.38 U/ml of CGTase were 55.8% and 5.92% corresponding to the increase of γ-amino butyric acid (GABA) and ferulic acid (FA) with 4.31 ± 0.68 mg/ml and 3.10 ± 0.02 mg/ml, respectively. The extract from MGBRF showed strong cytotoxic capacity against HepG2. Furthermore, the in vivo study revealed the stability of the glycemic index (GI) by consuming MGBRF with significant impacts on diabetes. These results suggest that MGBRF through the action of CGTase plays a major role in antidiabetes and HepG2 cell product value addition.