As the most important natural antioxidants in plant extracts, polyphenols demonstrate versatile bioactivities and are susceptible to oxidation. The commonly used ultrasonic extraction often causes oxidation reactions involving the formation of free radicals. To minimize the oxidation effects during the ultrasonic extraction process, we designed a hydrogen (H2)-protected ultrasonic extraction method and used it in Chrysanthemum morifolium extraction. Hydrogen-protected extraction improved the total antioxidant capacity, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, and polyphenol content of Chrysanthemum morifolium water extract (CME) compared with air and nitrogen (N2) conditions. We further investigated the protective effects and mechanisms of CME on palmitate (PA)-induced endothelial dysfunction in human aorta endothelial cells (HAECs). We found that hydrogen-protected CME (H2-CME) best-prevented impairment in nitric oxide (NO) production, endothelial NO synthase (eNOS) protein level, oxidative stress, and mitochondrial dysfunction. In addition, H2-CME prevented PA-induced endothelial dysfunction by restoring mitofusin-2 (MFN2) levels and maintaining redox balance.