Increasingly globally prevalent obesity and related metabolic disorders have underscored the demand for safe and natural therapeutic approaches, given the limitations of weight loss drugs and surgeries. This study compared the phytochemical composition and antioxidant activity of five different varieties of citrus physiological premature fruit drop (CPFD). Untargeted metabolomics was employed to identify variations in metabolites among different CPFDs, and their antilipidemic effects in vitro were assessed. The results showed that Citrus aurantium L. ‘Daidai’ physiological premature fruit drop (DDPD) and Citrus aurantium ‘Changshan-huyou’ physiological premature fruit drop (HYPD) exhibited higher levels of phytochemicals and stronger antioxidant activity. There were 97 differential metabolites identified in DDPD and HYPD, including phenylpropanoids, flavonoids, alkaloids, organic acids, terpenes, and lipids. Additionally, DDPD and HYPD demonstrated potential antilipidemic effects against oleic acid (OA)-induced steatosis in HepG2 hepatocytes and 3T3-L1 adipocytes. In conclusion, our findings reveal the outstanding antioxidant activity and antilipidemic effects of CPFD, indicating its potential use as a natural antioxidant and health supplement and promoting the high-value utilization of this resource.