Aberrant O-GlcNAc cycling of the cancer proteome is a manifestation of its metabolic plasticity. As one of the most common cancer of the female genital tract associated with metabolic syndrome, endometrial cancer (EC) tissues often bear altered O-GlcNAcylation patterns. However, integration of O-GlcNAc status with existing histomorphologic and molecular subtypes of EC in large cohorts and identification of molecular modules controlling the O-GlcNAc homeostasis remain to be accomplished. Here we establish a positive correlation of O-GlcNAcylation with histologic grade of EC in a Chinese cohort containing 219 tumors and consolidate it in The Cancer Genome Atlas (TCGA) EC dataset. Higher O-GlcNAc level is associated with less pathological differentiation and poorer prognosis. Functionally, increasing O-GlcNAcylation promotes proliferation and stem-like cell properties in normal endometrial epithelial organoids (EE-Os), whereas decreasing O-GlcNAcylation limits the growth of endometrial cancer organoids (EC-Os). Using genome-wide CRISPR screen, we further identify that the F-box only protein 31 (FBXO31), whose loss of heterozygosity is frequently observed in cancer, regulates O-GlcNAc homeostasis. FBXO31 acts as a substrate receptor of the SCF ubiquitin ligase complex to ubiquitinate the O-GlcNAc transferase OGT. Loss of FBXO31 results in accumulation of OGT and upregulation of O-GlcNAcylation in EC. Our study highlights the O-GlcNAcylation as a useful stratification marker and potential therapeutic target for the advanced, poorly differentiated EC cases.