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Intestinal stricture remains one of the most intractable complications in Crohn’s disease (CD), and the involved mechanisms are poorly understood. Accumulating evidence suggests that the gut microbiota contributes to the pathogenesis of intestinal fibrosis. In this study, we investigated specific mucosa-associated microbiota related to intestinal strictures and their role in predicting postoperative disease course. Twenty CD patients who had undergone operative treatments were enrolled and followed up. Intestinal mucosa and full-thickness sections from stenotic and non-stenotic sites were sterilely collected. DNA extraction and bacterial 16s rRNA gene sequencing were conducted. Radiological and histological evaluations were performed to assess fibrosis. Microbial alpha diversity was significantly decreased in stenotic sites (<i>p</i> = 0.009). At the genus level, <i>Lactobacillus</i>, <i>Oscillospira</i>, <i>Subdoligranulum</i>, <i>Hydrogenophaga</i>, <i>Clostridium</i> and <i>Allobaculum</i> were decreased in stenotic segments (<i>p</i> < 0.1). The difference in <i>Oscillospira</i> sp. (stenotic vs. non-stenotic) was negatively correlated with the erythrocyte sedimentation rate (correlation coefficient (CC) −0.432, <i>p</i> = 0.057) and white blood cell count (CC −0.392, <i>p</i> = 0.087) and positively correlated with serum free fatty acids (CC 0.575, <i>p</i> < 0.05). This difference was negatively associated with intestinal fibrosis evaluated by imagological and histological methods (CC −0.511 and −0.653, <i>p</i> < 0.05). Furthermore, CD patients with a higher abundance of <i>Oscillospira</i> sp. in the residual intestine might experience longer remission periods (<i>p</i> < 0.05). The mucosa-associated microbiota varied between stenotic and non-stenotic sites in CD. Most notably, <i>Oscillospira</i> sp. was negatively correlated with intestinal fibrosis and postoperative disease course. It could be a promising biomarker to predict post-operative disease recurrence and a microbial-based therapeutic target.