Saponins possess a variety of pharmacological effects and exhibit great potential in the food industry as bioactive substances. In this study, extracellular saponin production via the liquid fermentation of Tuber melanosporum occurred with the addition of rutin. For this purpose, medium composition and culture conditions were optimized using single-factor experiments and an orthogonal experiment design. The optimal medium consisted of glucose (43.5 g/L), peptone (6 g/L), KH2PO4 (1.15 g/L), NaCl (0.2 g/L), vitamin B2 (0.082 g/L), vitamin B6 (0.1 g/L), vitamin C (0.02 g/L), and rutin (4.8 g/L). The culture conditions were as follows: 12.5% (v/v) inoculation, medium volume of 50 mL/250 mL flask, culture temperature of 24 °C, shaker speed of 190 rpm, initial pH of 5.7, and culture time of 96 h. Finally, a maximal extracellular saponin content of 0.413 g/L was obtained, which was 134.7% higher than that in the base medium. Rutin proved to be an excellent promoter, because the saponin production was increased by 50.2% compared to that in the optimized medium without rutin. The 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging activity, hydroxyl radical scavenging activity, and ferric reducing antioxidant power of truffle saponins reached 94.13%, 79.26%, and 42.22 mM, respectively. This study provides a useful strategy for fungal bioactive saponin production by liquid fermentation with the addition of flavonoid compounds.