Background Laparoscopic common bile duct exploration (LCBDE) has gained wide popularity for the treatment of choledocholithiasis. However, it remains unclear whether LCBDE is a better alternative option for the patients with difficult biliary stones. Thus, the aim of the present study was to explore the safety and efficacy of LCBDE for these patients by retrospectively analyzing our data and combing with literature review. Methods Between September 2011 and February 2019, 1064 consecutive patients who underwent LCBDE at Shanghai Tenth People's Hospital were reviewed. The clinical data of patients with difficult biliary stones were selected and retrospectively analyzed. Results Of these patients, 334 cases were confirmed with difficult biliary stones, and the overall complete stone clearance rate was 98.8% (330/334). 34 cases (10.2%) were performed with laser lithotripsy. A total of 296 patients (88.6%) underwent primary closure of common bile duct, and T-tube drainage was indwelled in 38 patients (11.4%). No bile duct injury, bleeding, perforation and surgery-related deaths were observed. The overall morbidity rate was 6.6%. 16 cases (4.8%) occurred in bile leakage with primary closure procedure, and all of them were managed successfully with conservative therapy. The median follow-up period was 9 months with stone recurrence occurring in 9 patients (2.7%). There was no evidence of bile duct stricture in all cases. Conclusions The current study suggests that LCBED is a considerable safe and effective option for the patients with difficult biliary stones. A randomized clinical trial is needed to further evaluate the benefit of LCBDE in this subgroup.