The potentially beneficial effects of probiotics in the treatment of obesity have been generally demonstrated. In the present study, a new strain of Lactobacillus reuteri SY523 (L. reuteri SY523) with an anti-obesity effect was isolated from the fecal microbiota of diet-induced obese mice. Untargeted metabolomics analysis of mice serum showed that the significantly differential metabolite indole-3-carboxaldehyde (3-IAId) was markedly elevated in the L. reuteri SY523-treated group, and interestingly, the abundance of 3-IAId was significantly negatively associated with obesity-related indicators. As expected, in the HepG2 cell induced by free fatty acids, the potential activity of 3-IAId in restraining lipid deposition was verified. Further, we found that 3-IAId was involved in the anti-obesity effect of L. reuteri SY523 mainly via regulating the cGMP/cAMP signaling pathway. The highlight of this study lies in clarifying the pivotal role of metabolite 3-IAId in the anti-obesity effect induced by L. reuteri SY523, which is conducive to the development of probiotics for anti-obesity agents.