The aim of this paper was to prepare purified fractions of polysaccharides from jujube (Ziziphus jujuba Mill.) fruit and further compare their structural characteristics and antioxidant activities. Firstly, three purified jujube polysaccharides, named PZMP1, PZMP2 and PZMP3, were successfully prepared by DEAE-Sepharose Fast Flow and Sephacryl S-300 columns. Then, their characteristics were studied and then compared by using chemical testing, high-performance gel permeation chromatography (HPGPC), gas chromatography (GC), Fourier transform infrared spectroscopy (FT-IR), methylation analysis, NMR spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM) and atomic force microscopy (AFM). Thereafter, their antioxidant activities were also contrasted. The data achieved demonstrated that the three jujube polysaccharides derived from different adsorption capacity of DEAE-Sepharose Fast Flow and Sephacryl S-300 columns possessed different structural characteristics and antioxidant activity, and with higher galacturonic acid content could exhibit better antioxidant bioactivities, which could provide certain directions for the functional and medicinal purposes development of jujube polysaccharides.