Objective To compare the bile bacterial diversity in patients with different types of common bile duct stones (CBDS). Methods A total of 45 patients with CBDS diagnosed by abdominal ultrasound, abdominal CT and (or) magnetic resonance cholangiopancreatography (MRCP) and treated by endoscopic retrograde cholangiopancreatography (ERCP) in the First Affiliated Hospital of Air Force Medical University from August 2017 to January 2018 were divided into the non-stone (NS) group, the primary cholesterol stone (PCS) group, the primary pigment stone (PPS) group, and the recurrent stone (RS) group. 16S rRNA sequencing was used to analyze the microbile community structure and diversity in bile which was collected before contrast medium injection. Results Thirty-three patients were in the non-RS group (8 in the NS group, 8 in the PCS group, and 17 in the PPS group) and 12 were in the RS group. The proportion of patients with intra-diverticular papilla [41.67% (5/12) VS 3.03% (1/33),χ2=8.27,P=0.004], loose stones [91.67% (11/12) VS 36.36% (12/33), χ2=10.77, P=0.001] and pigmental stones [100.00% (12/12) VS 51.52% (17/33), χ2=7.04, P=0.008] were significantly higher in the RS group than those in the non-RS group. There was no significant difference in other baseline data (P>0.05). At the phylum and genus level, the bacterial abundance was similar in the RS and PPS group. Alpha and Beta diversity analysis showed that the microbial diversity was similar between the RS and PPS group, both of which were lower than those in the NS and PCS group (P<0.05). MetaStat analysis revealed that Helicobacter pylori was the dominant bacteria in the RS group, and Proteobacteria and Escherichia coli were the dominant bacteria in both RS and PPS groups. Conclusion Bacterial abundance of bile in the RS group is similar to that of the PPS group, but the diversity of biliary bacteria flora in the RS group and PPS group are significantly lower than those in the PCS group and NS group. Helicobacter pylori is the dominant biliary bacteria in the RS group.