To investigate the effects of Gastric bypass surgery on the apoptosis of islet β-cells in type 2 nonobese diabetic (NOD) rats and its mechanisms. Seventy-two 8-week-old GK rats were randomly divided into four groups:operation group (group O, n = 18), sham operation group (group S, n = 18), diet control group (group F, n = 18) and control group (group C, n = 18). The levels of fasting, postprandial blood glucose, insulin and glucagon-like peptide-1 (GLP-1) were measured and compared among the 4 groups before the operation and at 1, 2, 4 and 8 weeks following the operation. The blood samples were collected at 2, 4 and 8 weeks after the operation for the measurement of postprandial blood glucose, and then the rats in batches (6 rats in each group) were decapitated to retrieve the pancreas. The apoptosis of the islet β-cells was detected by using TUNEL assay, and the expression of apoptosis-related proteins Bcl-2, Bax was measured with immunohistochemistry. As for group O, the fasting blood glucose level decreased from (16.2 ± 0.8) mmol/L before the operation to respectively (9.2 ± 0.6) mmol/L and (9.7 ± 0.7) mmol/L at 4 and 8 weeks after the operation; postprandial blood glucose decreased from (31.1 ± 1.1) mmol/L before the operation to respectively (13.1 ± 0.7) mmol/L and (12.3 ± 0.7) mmol/L at 4 and 8 weeks after the operation. Fasting insulin level increased from (28.0 ± 1.2) mU/L before the operation to respectively (62.8 ± 1.9) mU/L and (61.7 ± 1.4) mU/L at 4 and 8 weeks after the operation; and at 4 and 8 weeks after the operation postprandial insulin level was (77.4 ± 1.1) mU/L and (77.1 ± 1.0) mU/L. At 2 weeks from the operation, the fasting GLP-1 in group O increased from (10.7 ± 1.0) pmol/L to (13.5 ± 0.8) pmol/L, and respectively to (26.1 ± 0.9) pmol/L and (25.3 ± 1.2) pmol/L at 4 and 8 weeks after the operation. The differences in the above-mentioned items before and after the operation were all significant in group O (P < 0.05), and the differences in the items among group O and the other three groups (P < 0.05) were all significant as well. In group O, the apoptosis rate of pancreatic islet cell decreased to (5.9 ± 0.7)% at 4 weeks from the operation, and (6.3 ± 1.1)% at 8 weeks from the operation (P < 0.05). The expression of Bcl-2 protein in group O was 31.3 ± 1.5, 35.7 ± 1.0 and 35.8 ± 0.8 at 2, 4 and 8 weeks post operation, which was significantly higher in statistics than those of the same time point in the other three groups (P < 0.05). The expression of Bax protein in group O was 13.3 ± 0.9, 10.8 ± 0.9 and 10.9 ± 1.1 at 2, 4 and 8 weeks from the operation, which was significantly lower in statistics than those of the same time point in the other three groups (P < 0.05). Gastric bypass surgery can significantly reduce the blood glucose level and promote the secretion of GLP-1, and therefore inhibit the apoptosis of the islet β cells in diabetic rats through the Bcl-2 pathway.