Lgr4/Gpr48 is one of the newly identified R-spondins receptors and potentiates Wnt signaling, which regulates intestinal homeostasis. We used a hypomorphic mouse strain to determine the role of Lgr4 in intestinal inflammation and recovery. Intestinal inflammation was induced with dextran sulfate sodium (DSS) followed by a recovery period. Intestinal inflammation symptoms and molecular mechanisms were examined. We found that Lgr4(-/-) mice exhibited dramatically higher susceptibility to and mortality from DSS-induced inflammatory bowel disease than WT mice. Lgr4 deficiency resulted in greatly reduced numbers of either Paneth cells or stem cells in the intestine. During the intestinal regeneration process, cell proliferation but not apoptosis of intestinal epithelial cells was significantly impaired in Lgr4(-/-) mice. When Wnt/β-catenin signaling was reactivated by crossing with APC(min)(/+) mice or by treating with a GSK-3β inhibitor, the number of Paneth cells was partially restored and the mortality caused by DSS-induced inflammatory bowel disease was strikingly reduced in Lgr4-deficient animals. Thus, Lgr4 is critically involved in the maintenance of intestinal homeostasis and protection against inflammatory bowel disease through modulation of the Wnt/β-catenin signaling pathway.