Background Roux-en-Y gastric bypass (RYGB) has been widely reported to be safe and feasible, and has a powerful effect on improving metabolism and weight loss in patients with a high body mass index (BMI). A few studies have focused on the comparison of RYGB with medical treatment in type 2 diabetes (T2D) patients with a lower BMI. Objectives To compare the metabolic effects and safety of RYGB versus medical treatment during a 2 years follow-up in T2D patients with a BMI of 25 to 32.5 kg/m(2). Methods This retrospective and multicenter cohort study participants were extracted from the T2D patients with a lower BMI (25-32.5 kg/m(2)) from three bariatric centers between 2009 and 2018. Propensity score matching (PSM) was used to minimize bias, and each patient in the surgical group was matched 1:2 to the patients in the medical group with the closest propensity score. Finally, 71 patients who received RYGB and 142 patients who underwent medical treatment with a 2 years follow-up were enrolled to compare the effects of RYGB and medical treatment. The primary endpoint was achievement of the triple endpoint (the simultaneous achievement of hemoglobin A1c (HbA1c) < 7.0%, fasting low-density lipoprotein cholesterol (LDL-C) < 100 mg/dL (2.6 mmol/L), and systolic blood pressure (SBP) < 130 mmHg at the year-1 visit). Changes in weight, BMI, medication usage, complications, and adverse events were assessed. Results In total, 213 patients (mean age of 47.4 +/- 9.5 years, 70.4% male, mean BMI of 28.6 +/- 2.2 kg/m(2)) were included in this study. At the end of the first year, 17 patients (23.9%) in the surgical group and 10 (7.0%) in the medical group had achieved the composite triple endpoint (OR 4.64; 95% CI 1.82-11.81; p = 0.001). Additionally, 43 patients (60.6%) in the surgical group and 11 patients (19.7%) in the medical group experienced remission of T2D. However, more complications were observed in the surgical group (36 vs. 22, p < 0.01). Conclusions Among T2D patients with a BMI between 25.0 and 32.5 kg/m(2), RYGB was more effective than medical treatment in resolving metabolic disorders and also resulted in more complications. The risk for complications should be considered in the clinical decision-making process for T2D patients with a low BMI.