Resistant starch (RS) is well known to prevent type 2 diabetes mellitus (T2DM) and obesity. Recently, attention has been paid to gut microbiota which mediates the RS's impact on T2DM and obesity, while a mechanistic understanding of how RS prevents T2DM and obesity through gut microbiota is not clear yet. Therefore, this review aims at exploring the underlying mechanisms of it. RS prevents T2DM and obesity through gut microbiota by modifying selective microbial composition to produce starch-degrading enzymes, promoting the production of intestinal metabolites, and improving gut barrier function. Therefore, RS possessing good functional features can be used to increase the fiber content of healthier food. Furthermore, achieving highly selective effects on gut microbiota based on the slight differences of RS's chemical structure and focusing on the effects of RS on strain-levels are essential to manipulate the microbiota for human health.