Background Endoscopic nasobiliary drainage (ENBD) was often used for preoperative biliary drainage in cases like cholangiocarcinoma or acute obstructive suppurative cholangitis, reports on endoscopic nasobiliary drainage (ENBD) over primary closure of the common bile duct (CBD) are limited. This study compares outcomes of laparoscopic cholecystectomy (LC) + laparoscopic CBD exploration (LCBDE) + intraoperative ENBD + primary closure of CBD with equivalent patients who underwent preoperative endoscopic retrograde cholangiopancreatography (ERCP) and subsequent LC. Methods From January 2013 to December 2015, 829 consecutive patients with choledocholithiasis combined with cholecystolithiasis underwent surgery in our department. 211 patients underwent LC + LCBDE + intraoperative ENBD + primary closure of CBD (group A) and 117 preoperative ERCP + subsequent LC (group B). A total of 501 patients (355 who underwent T-tube drainage and 146 who underwent transcystic exploration) were excluded from the analysis. Clinical records, operative findings, and postoperative follow-up were analyzed. Results Age and sex distribution, comorbidity, presentations, CBD diameter, and size and number of stones were similar in the two groups, and there was no postoperative mortality. Duration of surgery in group A was shorter (83 vs. 104 min, P< 0.01), as was postoperative hospital stay (6 vs. 9 days, P< 0.01). Average operative expenditure in group A was less than that of group B ($ 3816 vs. $ 4015, P< 0.01). The success rate in group A was higher (100 vs. 91%, P< 0.01). Ten patients in group B converted to LCBDE. The postoperative complication rate was higher in group B but without significant difference (1.9 vs. 4.2%, P = 0.29). Median follow-up time was 24 (3-28) months (n = 302 patients). Two patients in group B reported residual stones. Conclusion LC + LCBDE + intraoperative ENBD + primary closure of CBD should have priority over preoperative ERCP + subsequent LC for choledocholithiasis combined with cholecystolithiasis.