Background The recurrence of bile duct stones is a long-term outcome for patients undergoing laparoscopic common bile duct exploration (LCBDE) that is worthy of attention. This study aimed to investigate long-term risk factors for stones recurrence after LCBDE and develop a nomogram for predicting the risk. Methods The clinical data on consecutive patients with bile duct stones undergoing LCBDE at Shanghai Tenth People's Hospital between January 2014 and February 2019 with a follow-up period longer than 2 years were reviewed. Independent risk factors of stones recurrence identified by the Cox regression model were used to develop a nomogram in predicting stones recurrence after LCBDE. Results Eight hundred and twenty-two patients were eventually included in this study. Of these patients, 42 (5.11%) developed stones recurrence. The cumulative incidences of stones recurrence at 1, 3, and 5 years after LCBDE were 1.34%, 4.36%, and 7.14%, respectively. Independent risk factors of stones recurrence were identified to be age (HR = 1.04, 95% CI = 1.02-1.07), T-tube drainage (HR = 3.28, 95% CI = 1.23-8.72), fatty liver (HR = 2.69, 95% CI = 1.39-5.20), urinary calculus (HR = 4.68, 95% CI = 2.29-9.56), post-cholecystectomy (HR = 5.21, 95% CI = 2.39-11.33), and post-ERCP + EST (HR = 2.87, 95% CI = 1.18-6.96). By these factors, a developed nomogram showed a C-index of 0.770 to predict stones recurrence. Conclusions The nomogram, based on identified risk factors, showed good accuracy for predicting stones recurrence, which is valuable to guide these patients' follow-up and prevention.