Hemerocallis is a characteristic vegetable with outstanding edible and medicinal value. Flavonoids are important bioactive components of Hemerocallis. To improve the extraction efficiency and detection accuracy of flavonoids from Hemerocallis, we established a high-performance liquid chromatography (HPLC) detection system, which can simultaneously detect multiple flavonoids. In addition to the previously developed organic solvent extraction method, an ultrasonic-assisted extraction technique that uses fewer samples was established to extract flavonoids from Hemerocallis. The extraction conditions of the ultrasonic-assisted extraction were optimized via a single-factor experiment and a response surface experiment. The HPLC system detected and determined the contents of rutin, isoquercetin, myricetin, quercetin, apigenin, and diosmetin from 70 Hemerocallis germplasm resources. In addition, we evaluated the antioxidant activity of flavonoids in Hemerocallis using DPPH free radical scavenging capacity with ascorbic acid (Vc) as a positive control. The results showed that the optimum conditions for the ultrasonic extraction process were as follows: sample weight of 0.25 g, ethanol volume fraction of 72%, ethanol volume of 2.5 mL, and ultrasonic extraction time of 17 min. Under these conditions, flavonoid extraction had a strong scavenging effect on DPPH. With the increase in the sample solutions’ concentrations, its antioxidant capacity was gradually enhanced, and the DPPH scavenging rate reached 70.2%. The optimized ultrasonic-assisted extraction technology can increase the total content of six flavonoids in day lily bud by 59.01%, especially the content of rutin (increased by 64.41%) in Hemerocallis flower buds. Among 70 Hemerocallis plant resources, we selected materials H0087 and H0059 with high and stable flavonoid content, with the total content of six substances being 4390.54 ug/g and 3777.13 ug/g. Thus, this study provides a reference for extracting and determining flavonoid contents in Hemerocallis materials. It also provides a theoretical basis for high-quality individual plant breeding.