The link between gut microbiota and obesity or other metabolic syndromes is growing increasingly clear. Natural products are appreciated for their beneficial health effects in humans. Increasing investigations demonstrated that the anti-obesity bioactivities of many natural products are gut microbiota dependent. In this review, we summarized the current knowledge on anti-obesity natural products acting through gut microbiota according to their chemical structures and signaling metabolites. Manipulation of the gut microbiota by natural products may serve as a potential therapeutic strategy to prevent obesity.