Oral ecto-mesenchymal stem cells-conditional medium (EMSCs-CM) is a promising strategy for treating ulcerative colitis (UC). However, this therapy is currently limited by the harsh gastrointestinal environment and poor colonic targeting ability. Herein, a glutamine transaminase 2 (TG2) crosslinked EMSCs-CM hydrogel (EMSCs-CM-Gel) was fabricated by combining EMSCs-CM with negatively chargedγ-polyglutamic acid (γ-PGA) hydrogel. Intestinal epithelial cell 6 (IEC-6) was applied to construct a cell model with lipopolysaccharide to evaluate the anti-inflammatory potential of EMSCs-CMin vitro. The crosslinked gel was orally administered to mice in liquid form to access the effects of EMSCs-CM-Gelin vivo. This study was based on the fact that the hydrogel containing EMSCs-CM has negative charges, which ensure it remains at the positively charged inflamed colon tissue. The EMSCs-CM could continuously be released in the damaged colon mucosa along with the degradation of theγ-PGA hydrogel. Immunofluorescence and western blot were performed to assess the effects of EMSCs-CM-Gel on mice. The resultsin vivoshowed that EMSCs-CM-Gel could significantly suppress the expression of inflammatory cytokines, prevent the shortening of the length of the intestine and repair the intestinal barrier. Collectively, our findings provided a novel colon-targeted strategy, hoping to benefit UC patients a lot.