Obesity is a global pandemic and public health crisis over decades. Except for physical activity, dietary adjustments, pharmacotherapy and surgical interventions, prebiotics, which are believed to relieve obesity by modulating the host gut microbiota, have been a hot research area in recent years. Thus, in this study, our objective was to investigate the effects of Citrus aurantium L. 'Daidai' physiological premature fruit drop (DDPD) on obesity, and further explore whether the anti-obesity effects of DDPD relies on alterations in gut microbiota. Our findings revealed that supplementation with DDPD effectively alleviated HFD-induced obesity in mice, concomitantly reducing inflammation and oxidative stress. Moreover, DDPD reversed the imbalance of gut microbiota induced by HFD, enhancing beneficial bacteria associated with improved obesity, such as Bifidobacterium, Lachnospiraceae_NK4A136_group, Ruminococcus, and Muribaculaceae. Fecal microbiota transplantation demonstrated that DDPD-induced alterations in microbiota effectively mitigated weight gain and lipid abnormalities induced by HFD, while reshaping the microbiota composition of recipient mice to resemble that of donor mice. Notably, beneficial lipid metabolism bacterium Lachnospiraceae_NK4A136_group identified in donor mice successfully colonized in recipient mice. Additionally, transcriptomic analysis indicated that DDPD modulated lipid metabolism through regulating the expression of genes linked to Cpt1a, Agpat1, and Pnpla3. In conclusion, DDPD demonstrated promising anti-obesity properties, offering potential solutions to the global obesity epidemic.