Berries of Lycium barbarum L. are not only used for traditional Chinese medicine, but also for raw materials in many health foods. Polysaccharides are major components of L. barbarum berries, which possess a variety of biological activities. In this study, effects of water-soluble polysaccharides, in 8 typical batches of L. barbarum berries collected from different producing areas of China, on macrophage function were evaluated in vitro. Furthermore, to better understand the structure-activity relationship of the polysaccharides in L. barbarum berries, the activity of typical polysaccharides and their partial acid and enzymatic hydrolysates were also investigated and compared. The results showed that the effects of polysaccharides of different regions are similar, which should be correlated to their similar chemical properties. However, their promotion effects on macrophage function are different in degree, this might be caused by their different content of active polysaccharides. Moreover, the alpha-1,4-d-galactosiduronic and alpha-1,5-arabinosidic linkages, especially the former one was discovered to significantly affect the promotion effect on macrophage function induced by the polysaccharides in L. barbarum berries. These results were beneficial to improve the pharmacological activity-based quality control of polysaccharides in L. barbarum berries and their products.