<p>Intestinal fibrosis drives stricturing complications in Crohn’s disease (CD), yet the core stromal regulators remain incompletely defined. Here, we profile paired fibrotic and non-fibrotic ileum from CD patients using single-cell RNA sequencing and identify a selective expansion of fibroblasts enriched for an ECM-high transcriptional program. Among candidate transcription factors, PRRX1 was consistently upregulated in fibrotic regions and validated at transcript and protein levels. Functional interrogation using a Col1a2-Cre; Prrx1^fl/fl mouse model demonstrated that fibroblast-specific deletion of Prrx1 mitigated DNBS-induced fibrosis, confirming its pathogenic role in vivo. To complement this loss-of-function approach, we developed a PEGylated black phosphorus–alginate hydrogel (PRRX1@BP-PEG/Alg) for intrarectal delivery of recombinant PRRX1. This system exhibited high protein loading, mucosal adhesion, and controlled release. PRRX1 delivery reprogrammed human intestinal fibroblasts toward a matrix-producing phenotype, elevating FAP and COL1A1 expression and enriching profibrotic pathways. In vivo, PRRX1@BP-PEG/Alg exacerbated histological fibrosis and mesenchymal activation, as confirmed by colon proteomics. ChIP–seq and reporter assays further identified PRRX1 as a direct transactivator of the Fap promoter. Together, these data define a PRRX1–FAP regulatory axis driving fibroblast activation and intestinal fibrosis.</p> Graphical abstract <p></p>