The parameters for pressurized microwave-assisted extraction (PMAE) of total flavonoids (TFs) from Gnaphalium affine D. Don were investigated and the effect of PMAE on its cell wall and tissue structure was analyzed via scanning electron microscopy (SEM). Afterwards, its extraction effect was compared with that of microwave-assisted extraction (MAE), soxhlet extraction (SE) and heat reflux extraction (HRE). After purifying by AB-8 macroporous resin, the in vitro and in vivo antioxidant activities of purified TFs were evaluated by five different chemical assays and alcohol-induced model, respectively. Our findings revealed that an ethanol volume fraction of 81.3%, a L/S ratio of 25.4 mL/g and an extraction time of 138 s, give maximum yield of TFs (1.35 ± 0.02%). PMAE was more efficient and rapid in extracting TFs from G. affine because it cracked the cell wall and disrupted the tissue structure, as observed by SEM. Compared with microwave-assisted extraction (MAE), soxhlet extraction (SE) and heat reflux extraction (HRE), PMAE was more efficient and rapid technique for the extraction of TFs from G. affine. TFs from G. affine showed notable free radical, including 2,2-diphenyl-1-picrylhydrazyl (DPPH), superoxide anion, 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid)-diammonium salt (ABTS) cation, scavenging abilities and reduction ability in vitro. It could also significantly reduce the level of malondialdehyde (MDA), enhance the activity of superoxide dismutase (SOD) and total antioxidant capacity (T-AOC), and increase the level of glutathione (GSH) in the liver of mice with oxidative damage in a dose-dependent manner. Therefore, it showed good antioxidant capacity in vivo. TFs from G. affine indicated good in vitro and in vivo antioxidant activities, which suggests their potential in functional foods and pharmaceuticals as natural antioxidants agents.