M cells are specialized intestinal epithelial cells found in the follicle-associated epithelium (FAE) of Payer’s patches (PPs). M cells play a vital role, which is known as the gateway and initiator of mucosal immune responses in the gastrointestinal tract. Mature M cells, derived from intestinal stem cells, are randomly located throughout the gastrointestinal tract. The morphology of M cells is characterized by the lack of microvilli and a thin glycocalyx layer in comparison with other intestinal epithelial cells. Glycoprotein 2 (GP2) is highly expressed on the M-cells surface, to enable the uptake of pathogens in the lumen via ligand-receptor interactions. Then, antigens are transported to the subepithelial dome (SED) region to initiate IgA production. Therefore, applications targeting M cells have been attracting researchers’ attention. In this review, the origin, characteristics, and maturation of M cell were summarized, followed by discussion on the development of oral vaccines targeting M cells to solve the disadvantages of antigen dispersion in the intestine and immune tolerance in order to effectively stimulate the mucosal immunity in preventing intestinal pathogens. Furthermore, the combination of targeting M cell strategy and vaccine delivery system can not only effectively stimulate the mucosal immune but also protect the antigenic activity laying the base for research and development of oral vaccines in the future.