Background Emerging evidence suggests that epithelial cell-derived microRNAs (miRNA) are involved in the pathogenesis of inflammatory bowel disease; however, as of now specific implications in the real clinical practice, especially in relation to biologics use are yet far-fetched. Therefore, we tried to investigate specific epithelial cell derived miRNA signatures related to clinical and endoscopic activity in Crohn’s disease (CD) patients. Methods We prospectively collected terminal ileum tissue samples via ileocolonoscopy from healthy control (n=12), CD patients in remission (n=32) and active CD patients (n=36). CD remission was defined as clinical remission of Crohn's disease activity index (CDAI) <150 and achievement of endoscopic mucosal healing. Both inflamed and non-inflamed lesions were sampled in the active CD patients. Clinical information, medication use, chemistry data were measured within a week from the tissue sample date. miRNA levels were measured by small-RNA sequencing and qRT-PCR. Diagnostic ability of specific miRNA found were evaluated by receiver operating characteristic (ROC) curve analysis. Results The study cohort was followed up until January 2022. Mean follow-up period of the prospective CD cohort was 13.06 months. In comparing to the healthy control, CD patients in remission and active state revealed specific miRNA profiles in small-RNA sequencing. Through RT-PCR validation, we found that the expression levels of miR-141-3p, miR-338-3p, miR-378a-3p, and miR-200b-3p were significantly decreased, while miR-125b-5p, miR-29b-3p and miR-155-5p were significantly increased in the inflamed tissue of active CD patients. Moreover, in case of active CD patients, expressions of miR-150-5p, miR-200b-3p and miR-155-5p were significantly down-regulated in those using biologics, compared with biologics naïve patients. This may suggest that these miRNAs were not only as biomarkers of CD patients, but also as biomarkers related to inflammation and biologics response. ROC curve analysis suggested miRNAs with different diagnostic activity related to both clinical disease activity and endoscopic inflammation status. MiR-338-3p, miR-141-3p and miR-378a-3p demonstrated area under curve of greater than 0.9 in predicting active CD patients. Conclusion We report specific miRNA biomarkers identifying CD and its disease inflammation activity with relation to biologics use, suggesting potential treatment target in CD pathogenesis. These miRNA signatures could also be of potential clinical use in positioning biologics, which we intend to explore in the near future.