<p>Gut microbiota plays a critical role in bile acid (BA) metabolism within healthy populations, yet the differential species involved in BA metabolism in patients with Crohn’s disease (CD) remains poorly characterized. To address this knowledge gap, we conducted a comparative metagenomics for nine CD patients and nine healthy controls. Integrated metagenomic species profiling and functional annotation, accompanied with species-function network analysis, reduced abundance in metabolism-associated genes and lower species-function correlation were predicted, suggesting a possible imbalance of microbial communities in CD group. Focused on functional genes involved in BA metabolism and their associated bacterial taxa, our results revealed that <i>Anaerostipes hadrus</i>-like (<i>P</i> = 0.001317), <i>Roseburia intestinalis</i>-like (<i>P</i> = 0.03542), and <i>Coprococcus catus</i>-like (<i>P</i> = 0.0005787), the microbial species related to bile salt hydrolase-coding gene, showed significantly lower abundance in CD patients. Conversely, <i>Ruminococcus gnavus</i>-like, related to 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes, demonstrated relatively higher abundance (<i>P</i> = 0.0257). <i>Escherichia coli</i>-like, the species for 7α-HSDH-coding genes, also exhibited higher abundance in CD group (<i>P</i> = 0.01044). Further network correlation analysis indicated that there was a potential association between these differential species with other co-occurring gut microbiota. Collectively, the findings identify and characterize the differential gut microbiota involved in BA metabolism in CD patients, which may provide the possible target microorganisms for future therapeutic interventions.</p>