The incidence of depressive disorders has steadily increased, with factors such as social stress, neuroinflammation, and gut dysbiosis contributing to the intricate pathogenesis of depression. Traditional antidepressants often exhibit limited efficacy and are accompanied by pharmacological side effects. Moringa isothiocyanate-1 (MITC-1), a food-medicinal active substance isolated from moringa seeds, has demonstrated anti-inflammatory and neuroprotective properties. However, the potential effects and the mechanism of MITC-1 on neuroinflammation associated with depression remain unclear. In this study, we characterized aberrant activation of microglia induced by lipopolysaccharides (LPS) and demonstrated that MITC-1 has a protective effect on gut dysbiosis and neuroinflammation. We found that in MITC-1 treated mice, neuroinflammation was attenuated, evidenced by increased interest in sucrose and food rewards, reduced ingestion latency, enhanced novel object recognition, and improved voluntary activity and social behaviors. Subsequently, fecal microbiota transplantation (FMT) models were also established in mice, primarily focusing on behavioral aspects and intestinal function evaluations. We found fecal microbiota transplantation from MITC-1 treated mice facilitated the reconstruction of gut microbiota in LPS-induced mice. Ultimately, integrative approaches utilizing gut microbiome and metabolomics technology analyses, coupled with neuroglial morphology assessments, were employed to uncover the preventive mechanisms of MITC-1 against inflammatory depression. Our results revealed that oral administration of MITC-1 significantly altered the fecal microbiota composition, up-regulated the tryptophan (Trp) metabolic pathway, and inhibited neuronal loss and microglial activation, thereby, ameliorating mood, cognition function, and behaviors. In summary, MITC-1 mediated the microbiota-gut-brain axis through the Trp metabolic pathway, restructuring gut microbes and reducing neuroinflammation.