L. indica L. cv. Mengzao, a medicinal plant of the Ixeris genus, is rich in flavonoids. In order to thoroughly analyze the the distribution and dynamic change of major flavonoids in its various parts from different growth periods, the flavonoids extracted from L. indica L. cv. Mengzao were identified and quantitatively analyzed by ultra-high-performance liquid chromatography mass spectrometer (LC-MS/MS). Results indicated that 15 flavonoids were identified from L. indica L. cv. Mengzao, and rutin, luteolin, luteolin-7-O-glucoside, kaempferol, quercetin, and apigenin are the major flavonoids in L. indica L. cv. Mengzao. In general, the total flavonoids’ content in different parts of L. indica L. cv. Mengzao followed the order flowers > leaves > stems > roots. Flowers and leaves are the main harvesting parts of L. indica L. cv. Mengzao, and the flowering period is the most suitable harvesting period. This study provides valuable information for the development and utilization of L. indica L. cv. Mengzao and determined the best part to harvest and the optimal time for harvesting.