The association between non-alcoholic fatty liver disease and hepatitis B virus (HBV) infection is inconclusive. The aim of this study was to investigate the viral dynamic of HBV and its association with change of body mass index (BMI), aspartate transaminase (AST), and alanine transaminase (ALT) levels after bariatric surgery. Patients who underwent bariatric surgery between June 2011 and May 2014 were selected in this retrospective study. BMI, AST, ALT, and HBV DNA levels were calculated pre-operatively and at 1st, 3rd, and 6th postoperative months. Two hundred and seventy-nine patients including 34 (12.2%) HBsAg-positive and 245 (87.8%) HBsAg-negative patients were enrolled. Eighteen HBsAg-positive and HBeAg-negative patients were matched with 36 HBsAg-negative patients. A significant decrease in BMI was found since 1st postoperative month in both groups. AST and ALT increased at 1st postoperative month, but decreased at 3rd and 6th postoperative months in both groups. However, a significant increase in HBV DNA level was observed in HBeAg-negative patients since 1st postoperative month with the highest peak at 3rd postoperative month. HBV reactivation occurred in 4 out of 17 (23.5%) patients, 8 out of 16 (50.0%) patients, and 4 out of 12 (33.3%) patients at 1st, 3rd, and 6th postoperative months, respectively. The change of HBV DNA was not associated with change of BMI, AST, or ALT after bariatric surgery. Bariatric surgery can achieve significant weight loss and improvement of liver function tests. However, there existed significant risk of HBV reactivation after bariatric surgery for patients with obesity.