Abstract Background Lipid metabolism disorder is a critical feature of Crohn’s disease (CD). We previously reported that phosphatidylinositol (PI), and its derivative phosphatidylinositol bisphosphate (PIP2) were significantly associated with CD activity. The underlying mechanisms remained unknown. We aimed to explore the function of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2], the major PI derivative, in modulating CD pathogenesis. Methods Lipidomics was used to analyse the relationship between CD activity and PI or PIP2. The mucosal expression of PI(4,5)P2 in patients with CD was measured by immunofluorescence. Dextran sodium sulfate (DSS)-induced colitis mice and lipopolysaccharide (LPS)-induced Caco-2 cell model were established to explore the function and mechanism of PI(4,5)P2. MeRIP and mRNA sequencing were applied to further reveal the mechanism of PI(4,5)P2. Results Lipid PIP2 was substantially negatively associated with disease activity and high-sensitivity C-reactive protein. PI(4,5)P2 expression was downregulated in the inflamed mucosa of patients with CD. PI(4,5)P2 alleviated mice colitis, with improvements in survival rate, colon length, body weight, and disease activity index. PI(4,5)P2 also alleviated DSS-induced tissue damage, tight junction loss, and intestinal epithelial cell (IEC) pyroptosis. In the in vitro LPS-induced cell model, PI(4,5)P2 inhibited pyroptosis, NLRP3, and caspase-1 expression, and reduced IL-18, IL-1β, and lactate dehydrogenase (LDH) secretion. PI(4,5)P2 mediated NNMT upregulation in mice and Caco-2 cells. NNMT knockdown restricted the inhibitory effect of PI(4,5)P2 on IEC pyroptosis. NNMT inhibited the stability of RBP4 mRNA via the m6A modification to prevent pyroptosis upon PI(4,5)P2 treatment. Conclusion PI(4,5)P2 inhibited IEC pyroptosis through NNMT-mediated RBP4 m6A modification, which ameliorating colitis. PI(4,5)P2 may be a therapeutic target for CD.