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Background Spasmolytic polypeptide expressing metaplasia (SPEM) is a precancerous lesion. We demonstrated selective deletion of Slc26a9 induced parietal cells (PCs) pyroptosis, followed by activating the IL-25–ILC2–M2 macrophage axis to induce SPEM. But the contribution of stromal cells within the SPEM-associated microenvironment remains poorly defined. This study aims to elucidate how epithelial-stromal-immune cells crosstalk collaboratively induce SPEM.Methods Slc26a9fl/fl mice were crossed with H+-K+-Atp4b-Cre to produce the PCs-specific Slc26a9 knockout in Slc26a9fl/fl/Atp4b-Cre mice in a mixed genomic background. A multi-method approach was employed, including scRNA sequencing, metabolomics, ELISA, Westernblot (WB) and Immunofluorescence (IF).Results Single-cell RNA sequencing of gastric tissues from Slc26a9fl/fl and Slc26a9fl/fl/Atp4b-Cre mice identified five subsets of mesenchymal cells, among which a novel Apoe+Pdgfra+ subset was markedly expanded following conditional Slc26a9 deletion. Differential expression analysis revealed that Apoe+Pdgfra+ fibroblasts exhibited marked upregulation of classic cancer-associated fibroblast (CAF) marker genes, including Col12a1, Col27a1, Col6a3, and Tgfbi, which was further validated by WB and IF. Functional enrichment analysis indicated their active involvement in pathways related to cell proliferation and migration. These results demonstrated that fibroblasts begin to transition to CAF phenotype as early as the SPEM stage after PCs-specific Slc26a9 deletion. Furthermore, non-targeted metabolomics revealed disrupted beta-Alanine metabolism and a significant increase in tissue spermidine levels in Slc26a9-deficient mice. In vitro stimulation of primary mouse fibroblasts with spermidine induced Stat3 phosphorylation and subsequent Apoe upregulation. This spermidine-induced Apoe expression was abolished by Stat3 phosphorylation inhibitor, demonstrating that the effect was Stat3-dependent. Cell-chat analysis revealed Apoe+Pdgfra+ fibroblasts interact with macrophages via the Col6a5-Sdc4 ligand-receptor pair. IF assay indicated that this interaction drives macrophage M2 polarization, which was confirmed by the upregulation of Col6a5 and Sdc4 in Slc26a9fl/fl/Atp4b-Cre mice, where Col6a5 was co-localized with Apoe and Sdc4 was co-localized with the M2 macrophage marker CD163.Conclusions PCs specific Slc26a9 deletion drives SPEM by expanding Apoe+Pdgfra+ fibroblasts via the spermidine-Stat3 axis, and promotes macrophage M2 polarization via the Col6a5-Sdc4 ligand-receptor pair.