The structural characteristics, acetylcholinesterase inhibitory activity, and immune effects of two purified acid polysaccharides from Chrysanthemum morifolium cv. Gongju were investigated. GJP-1 and GJP-2 were isolated and purified using DEAE-sepharose and Sephadex G-100 chromatography. GJP-1 consisted of Man, Rha, Ara, Glc, Gal, and GalA, with a ratio of 1.99:3.98:81.2:2.65:7.03:3.15, while GJP-2 comprised of Man, Rha, Ara, Glc, Gal, and GalA in a ratio of 0.27:2.36:8.03:38.44:2.38:48.52. GJP-2 is a kind of pectin-type polysaccharide. GJP-1 and GJP-2 differed in average molecular weight of 5.86 kDa and 4.92 kDa. The results indicated that GJP-1 and GJP-2 significantly inhibited the activity of acetylcholinesterase and had good immunomodulatory activities. GJP-1 and GJP-2 are bioactive polysaccharides with the potential to improve cognitive function. GJP-2 promoted more proliferation, as well as the release of tumor necrosis factor-α and interferon γ. Clarifying the structures and bioactivities of polysaccharides could lay a foundation for the application of Gongju in functional foods and medicines production.