Abstract: This study aimed to investigate the effects of flavonoids of finger citron from Guangdong Province (CF) on the gel properties, antioxidant activities, and metabolomic profile of yogurt. The impact of CF on the gel properties of yogurt was analyzed by measuring its water-holding capacity, texture, and rheological properties. The effects of adding CF before and after fermentation on yogurt's antioxidant activities were evaluated, and the influence of CF on the microstructure of yogurt was investigated using scanning electron microscopy. Fourier-transform infrared (FTIR) spectroscopy and circular dichroism (CD) spectroscopy were employed to elucidate the interactions between CF and both casein and whey proteins in yogurt. Additionally, non-targeted metabolomics was employed to analyze the changes in metabolites. The results showed that the addition of CF significantly improved the water-holding capacity of yogurt (P<0.05), with a 10.76% increase in water-holding capacity observed in CF-enriched yogurt compared to the control group after 21 days of storage. In terms of texture, the addition of CF significantly improved the hardness, cohesiveness, and viscosity of yogurt (P<0.05). The addition of CF also significantly increased the apparent viscosity of yogurt (P<0.05), enhancing its gel properties. The addition of CF also enhanced the antioxidant activity of yogurt, with the pre-fermentation incorporation showing greater effectiveness than post-fermentation addition. Specifically, yogurt containing CF added before fermentation exhibited increases of 92.84%, 459.82%, and 143.10% in DPPH and ABTS⁺ radical scavenging rates and ORAC values, compared to the control group and yogurt with CF added after fermentation, which showed increases of 9.02%, 12.45%, and 21.49%, respectively. Yogurt enriched with CF exhibited a more uniform and denser microstructure compared to the control group, along with changes in the conformations of whey proteins and casein, which may explain the enhanced water-holding capacity. Non-targeted metabolomics revealed significant changes in various metabolites in yogurt due to the addition of CF, with a decrease in 20 metabolites and an increase in 16 metabolites, particularly a significant reduction in chalcones and isoflavones (P<0.05). CF primarily influenced amino acid and phenylalanine metabolism, which played a significant role in the antioxidant properties of flavonoid-enriched yogurt. This study provides theoretical support for the application of CF as a functional active ingredient in yogurt.