<p>How intestinal stem cells (ISCs) are regulated during inflammation remains largely unexplored, leading to a lack of effective treatments for inflammatory bowel diseases (IBD). ISC-mediated intestinal epithelial regenerative repair can be regulated by intra-epithelial T lymphocytes, whose maturation is controlled by STAT5 dimeric or tetrameric activation. However, the mechanisms by which the T lymphocytes can protect ISCs are unclear. Here we hypothesize that tetrameric STAT5 regulates intra-crypt T cells to act as niche cells for ISC regeneration. Using IBD biospecimens, STAT5-hyperactive, tetramer-deficient mice and organoids, we found IBD–ulcerative colitis exhibited more crypt TCRγδ⁺STAT5⁺ T cells and less ISC pluripotency than healthy patients. Compared with wild-type mice, depleting tetrameric STAT5 in mice significantly increased ISC-mediated intestinal epithelial hyperplasia, TCR gene signatures, crypt TCRγδ⁺ T cells with elevated STAT5 tyrosine phosphorylation (pYSTAT5) and IL-17A levels, amplified both Lgr5^hi and Lgr5^low ISC proliferation and promoted de novo crypt regeneration with increased TCRγδ⁺ cell influx post irradiation or colitis. By contrast, depleting tetrameric STAT5 in organoids reduced ISC pluripotency and organoid growth post irradiation. Mechanistically, chromatin immunoprecipitation and single-cell RNA sequencing analyses with crypt cells revealed that depleting STAT5 tetramers decreased STAT5-binding on the <i>Metallothionein 1</i> (<i>Mt1</i>) locus in crypt T cells and increased <i>Mt1</i> expression, which leads to T cell migration into crypts and enhanced ISC regeneration. Together, the tetrameric STAT5 suppresses the formation of the crypt T cell niche. Interrupting STAT5 tetramers promotes the expansion of crypt TCRγδ cells, providing a target for promoting ISC regenerative repair during IBD–ulcerative colitis.</p>