Polysaccharides are considered to be the most important active substances in Goji. However, the structure of polysaccharides varies according to the extraction methods applied, and the solution used to prepare Goji polysaccharides (LBPs) were limited. Thus, it is important to clarify the connection between extraction methods and structure of Goji polysaccharide. In view of the complex composition of cell wall polysaccharides and the various forms of interaction, different extraction methods will release different parts of the cell wall. The present study compared the effects of different extraction methods, which have been used to prepare different types of plant cell wall polysaccharides based on various sources, on the structure of cell-wall polysaccharides from Goji, by the single separate use of hot water, hydrochloric acid (0.4%) and sodium hydroxide (0.6%), at both high and low temperatures. Meanwhile, in order to explore the limitations of single extraction, sequential extraction methods were applied. Structural analysis including monosaccharide analysis, GPC-MALLS, AFM and 1H-NMR suggested the persistence of more extensively branched rhamnogalacturonan I (RG-I) domains in the procedures involving low-temperature-alkali, while procedures prepared by high-temperature-acid contains more homogalacturonan (HG) regions and results in the removal of a substantial part of the side chain, specifically the arabinan. A kind of acidic heteropolysaccharide was obtained by hot water extraction. SEC-MALLS and AFM confirmed large-size polymers with branched morphologies in alkali-extracted polysaccharides. Our results provide new insight into the extraction of Goji polysaccharides, which differ from the hot water extraction used by traditional Chinese medicine.