Pancreatic damage, in the form of pancreatitis, intestinal bacteria and glucose imbalance could be interrelated. The aim of this study was to investigate the breath hydrogen (H2) and methane (CH4), which can indicate small intestinal bacterial overgrowth (SIBO) status, and assess the link between SIBO and glucose tolerance in patients with acute pancreatitis (AP). This prospective study enrolled 75 patients who were admitted for AP. A glucose breath test (GBT) which detects breath hydrogen H2 and CH4 for SIBO with an oral glucose tolerance test (OGTT) for 120 min was simultaneously performed to determine SIBO and glucose tolerance. Patient demographic data, laboratory test data, and computed tomography severity index (CTSI) were also evaluated. The levels of total breath H2 and CH4 in patients with AP were significantly higher than those in controls, respectively (p < 0.01). There were no significant differences in the incidence of SIBO between patients with AP and controls. The OGTT indicated that blood glucose levels at 30, 60, 90, and 120 min were higher in SIBO-positive patients than in SIBO-negative patients. No significant differences in CTSI, patient demographic data or laboratory test data were observed between the two groups. Breath H2 and CH4 concentrations are relatively higher in patients with AP, indicating a correlation between high levels of intestinal bacteria and AP. Furthermore, higher breath H2 and CH4 concentrations appear to be associated with oral glucose intolerance, with hyperglycemia occurring in patients with AP.