In this study, three novel and natural polysaccharides (FMP-1, FMP-2, and FMP-3) were obtained from Flos Magnoliae (FM, Xinyi in Chinese) using an efficient and green technique (hot-compressed water) for extraction and purified by DEAE-52 and Sephadex G-150. Their physicochemical properties, morphological and structural characteristics were investigated using chemical methods and instrumental analysis including methylation, partial acid hydrolysis, STA, GC-MS, HPGPC, HPAEC, FT-IR and NMR (1D and 2D). Results showed that FMPs all contained arabinose, rhamnose, galactose, xylose, mannose and galacturonic acid. FMP-2, with the highest yield and average molecular weight of the three (278.69 kDa), had large amounts of RG-I, minor amounts of HG with the molar ratio of 83.5:10.4, and trace amounts of RG-II domains. Thermal analys is exhibited that FMP-2 has a favorable thermal stability and it also exhibited effective antioxidant activities in a dose-dependent manner, which could be used as a potential stabilizer, thickening agent and natural antioxidant. These investigations provide a scientific basis for further investigation of FM polysaccharides in the context of their potential application in functional foods and medicines.