Inflammatory bowel disease (IBD) is a chronic inflammatory disorder in the intestines without a cure. Current therapies suppress inflammation to prevent further intestinal damage. However, healing already damaged intestinal epithelia is still an unmet medical need. Under physiological conditions, Lgr5 intestinal stem cells (ISCs) in the intestinal crypts replenish the epithelia every 3-5 days. Therefore, understanding the regulation of Lgr5 ISCs is essential. Previous data suggest vitamin D signaling is essential to maintain normal Lgr5 ISC function in vivo. Our recent data indicate that to execute its functions in the intestines optimally, 1,25(OH)D requires high concentrations that, if present systemically, can cause hypercalcemia (i.e., blood calcium levels significantly higher than physiological levels), leading to severe consequences. Using 5-bromo-2'-deoxyuridine (BrdU) to label the actively proliferating ISCs, our previous data suggested that de novo synthesized locally high 1,25(OH)D concentrations effectively enhanced the migration and differentiation of ISCs without causing hypercalcemia. However, although sparse in the crypts, other proliferating cells other than Lgr5 ISCs could also be labeled with BrdU. This current study used high-purity Lgr5 ISC lines and a mouse strain, in which Lgr5 ISCs and their progeny could be specifically tracked, to investigate the effects of de novo synthesized locally high 1,25(OH)D concentrations on Lgr5 ISC function. Our data showed that 1,25(OH)D at concentrations significantly higher than physiological levels augmented Lgr5 ISC differentiation in vitro. In vivo, de novo synthesized locally high 1,25(OH)D concentrations significantly elevated local 1α-hydroxylase expression, robustly suppressed experimental colitis, and promoted Lgr5 ISC differentiation. For the first time, this study definitively demonstrated 1,25(OH)D's role in Lgr5 ISCs, underpinning 1,25(OH)D's promise in IBD therapy.