Impairment of the intestinal mucosal immunity significantly increases the risk of acute and chronic diseases. Immunoglobulin A (IgA) plays a major role in humoral mucosal immunity to provide protection against pathogens and toxins in the gut. Here, we investigated the role of endogenous galectin-9, a tandem repeat-type β-galactoside–binding protein, in intestinal mucosal immunity. By mucosal immunization of Lgals9−/−and littermate control mice, it was found that lack of galectin-9 impaired mucosal antigen-specific IgA response in the gut. Moreover, Lgals9−/− mice were more susceptible to developing watery diarrhea and more prone to death in response to high-dose cholera toxin. The results indicate the importance of galectin-9 in modulating intestinal adaptive immunity. Furthermore, bone marrow chimera mice were established and galectin-9 in hematopoietic cells was found to be critical for adaptive IgA response. In addition, immunized Lgals9−/− mice exhibited lower expression of Il17 and fewer TH17 cells in the lamina propria, implying that the TH17–IgA axis is involved in this mechanism. Taken together, these findings suggest that galectin-9 plays a role in mucosal adaptive immunity through the TH17–IgA axis. By manipulating the expression or activity of galectin-9, intestinal mucosal immune response can be altered, and may benefit the development of mucosal vaccination.