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Plant polysaccharides exhibit many biological activities that are remarkably affected by molecular size and structures. This study aimed to investigate the degradation effect of ultrasonic-assisted Fenton reaction on the Panax notoginseng polysaccharide (PP). PP and its three degradation products (PP3, PP5, and PP7) were obtained from optimized hot water extraction and different Fenton reaction treatments, respectively. The results showed that the molecular weight (Mw) of the degraded fractions significantly decreased after treatment with the Fenton reaction. But the backbone characteristics and conformational structure were similar between PP and PP-degraded products, which was estimated by comparing monosaccharides composition, functional group signals in FT-IR spectra, X-ray differential patterns, and proton signals in 1H NMR. In addition, PP7, with an Mw of 5.89 kDa, exhibited stronger antioxidant activities in both the chemiluminescence-based and HHL5 cell-based methods. The results indicated that ultrasonic-assisted Fenton degradation might be used to improve the biological activities of natural polysaccharides by adjusting the molecular size.