Abstract: To realize the high-value utilization of Cistanche deserticola residue resources, the residue remaining after the extraction of phenylethanoid glycosides from Cistanche deserticola was used as the raw material in this study. The differences in chemical structural characteristics and antioxidant activities of different polysaccharide fractions graded by membrane separation were systematically explored. The results showed that significant differences existed in the chemical composition and biological activity of polysaccharide fractions with different molecular weights. Four polysaccharide fractions with distinct molecular weight ranges were successfully prepared using ultrafiltration membranes with different molecular weight cutoffs (300 kDa, 50 kDa, and 10 kDa) combined with ethanol precipitation, including CTP1 (molecular weight>300 kDa), CTP2 (50~300 kDa), CTP3 (10~50 kDa), and CTP4 (<10 kDa). Monosaccharide composition analysis demonstrated that the four fractions were mainly composed of mannose, rhamnose, galacturonic acid, glucose, galactose, and arabinose, with distinct molar ratios of monosaccharides among different fractions. Fourier-transform infrared spectroscopy confirmed that all fractions exhibited typical characteristic absorption peaks of polysaccharides. Scanning electron microscopy observations revealed that ultrafiltration membranes with different pore sizes significantly altered the aggregation state and surface roughness of polysaccharides by intercepting polysaccharide components with different molecular weights. Such morphological differences were related to the intermolecular forces of polysaccharides and the sieving effect during the ultrafiltration process. In antioxidant activity tests, CTP1 presented the optimal antioxidant performance. At a concentration of 8 mg/mL, the DPPH and ABTS·⁺ radical scavenging rates of CTP1 exceeded 61% and 95%, respectively. All four fractions exhibited certain antioxidant activity. This study verified that membrane separation technology could effectively fractionate polysaccharides from Cistanche deserticola residues. The research provided theoretical basis and data support for the resource recycling of traditional Chinese medicine residues and the high-value development of polysaccharide components.