BACKGROUND: Gastric cancer (GC) represents a significant therapeutic challenge due to its aggressive progression and limited treatment options, emphasizing the urgent need for novel therapeutic targets and strategies. Although PYGO1 functions as a Wnt co-transcriptional activator and chromatin effector, its role in cancer remains poorly characterized. This study aims to elucidate the role of PYGO1 in GC and uncover its regulatory mechanisms. METHODS: Bioinformatics analysis and immunohistochemistry were used to assess PYGO1 expression in GC tissues and its correlation with prognosis and immune cell infiltration. Cellular and animal models were applied to validate the role of PYGO1 in GC. RNA sequencing, flow cytometry, and immunofluorescence explored the underlying mechanisms. Co-immunoprecipitation coupled with mass spectrometry identified PYGO1-interacting proteins. Molecular docking and molecular dynamics simulations screened and evaluated potential PYGO1 inhibitors. RESULTS: PYGO1 was significantly overexpressed in GC tissues and positively correlated with M2 macrophage infiltration and adverse prognosis. Its knockdown significantly inhibited GC cell proliferation, migration, and invasion in vitro, and reduced tumor growth and metastasis in vivo. Mechanistically, PYGO1 knockdown impaired cell adhesion and disrupted cytoskeletal integrity in GC cells via downregulation of the ITGB1/CD47 axis, mediated by the interaction of PYGO1 with H3K4me(2/3), rather than BCL9. Pentagalloylglucose (PGG) disrupted the PYGO1-H3K4me(2/3) interaction, suppressing the ITGB1/CD47 axis and GC malignancy. CONCLUSIONS: Our study demonstrates the oncogenic role of PYGO1 in GC and identifies PGG as a potential inhibitor, highlighting the PYGO1/ITGB1/CD47 axis as a promising therapeutic target for GC.