Objective To compare the changes of biliary microbiota after enteral extended biliary stents (EEBS) implantation with that of conventional plastic stents in animal experiment, and to preliminarily investigate its possible mechanism in preventing stents occlusion. Methods A total of 12 healthy Bama minipigs were randomly assigned to the conventional plastic stent group (n=6) and the EEBS group (n=6) using simple random method. The bile samples of all pigs were collected before stents implantation and 4 weeks after stents placement. The biliary microbiota composition and diversity before and after different stents implantation were analyzed by 16S rRNA gene sequencing and compared. Results No complications including acute cholangitis, perforation, bleeding, or death occurred in 12 pigs. Eight days after stents implantation, stents were out of bile duct in all pigs under endoscopy, while the bile samples were collected again for analysis. The main composition of biliary microbiota at the phylum level were Proteobacteria, Firmicutes and Bacteroidota. Alpha-diversities revealed the Shannon (P=0.004) and Simpson index (P=0.008) significantly decreased in the conventional stent group after stents placement, and Bata diversity analysis also showed a significant difference in microbial composition (Anosim: R=0.514 8, P=0.011). There was no significant difference in Observed species index (P=0.095), Chao1 index (P=0.136), Shannon index (P=0.353), Simpson index (P=0.227) or Bata diversity (Anosim:R=0.059 3,P=0.187) in the EEBS group before and after stents placement. LEfSe algorithm indicated Bacteroides_fragilis and Proteobacteria⁃Gammaproteobacteria‑Enterobacterales‑Enterobacteriaceae‑scherichia_Shigella‑Escherichia_coli significantly increased in the conventional stent group, and Desulfobacterota⁃Desulfovibrionia⁃Desulfovibrionales⁃Desulfovibrionaceae‑Bilophila significantly increased in the EEBS group after stents placement. Conclusion The biliary microbiota change slightly after EEBS implantation in the short-term, and EEBS may prevent duodenobiliary reflux by prolonging the reflux path.