Cholelithiasis is a kind of common and multiple diseases. In recent years, traditional laparotomy has been challenged by a minimally invasive surgery. Through literature review, the therapeutic method, effect, and complications of minimally invasive treatment of intrahepatic and extrahepatic bile duct stones by combining our practical experience were summarized as follows. (1) For intrahepatic bile duct stones, the operation may be selected by laparoscopic liver resection, laparoscopic common bile duct exploration (LCBDE), or percutaneous transhepatic cholangioscopy. (2) For concomitant gallstones and common bile duct stones, the surgical approach can be selected as follows: laparoscopic cholecystectomy (LC) combined with endoscopic sphincterotomy (EST) or endoscopic papillary balloon dilatation, LC plus laparoscopic transcystic common bile duct exploration, LC plus LCBDE, and T-tube drainage or primary suture. (3) For concomitant intrahepatic and extrahepatic bile duct stones, laparoscopic liver resection, choledochoscopy through the hepatic duct orifice on the hepatectomy cross section, LCBDE, EST, and percutaneous transhepatic cholangioscopic lithotripsy could be used. According to the abovementioned principle, the minimally invasive treatment approach combined with the surgical technique and equipment condition will be significant in improving the therapeutic effect and avoiding the postoperative complications or hidden dangers of intrahepatic and extrahepatic bile duct stones.