Here, a pectin LBP1C-2 with the molecular weight of 99.8 kDa was purified from fruits of Lycium barbarum L. Its structure was elucidated as a backbone of alternate 1, 2-linked α-Rhap and 1, 4-linked α-GalpA, with branches of terminal (T) -, 1, 3-, 1, 6- and 1, 3, 6-linked β-Galp, T-, 1, 5- and 1, 3, 5-linked α-Araf and T-linked β-Rhap substituted at C-4 of 1, 2, 4-linked α-Rhap. The cell-based experiments indicated that LBP1C-2 suppressed Aβ42 production in a dose-dependent manner with no cytotoxicity. Further study showed that expression of β-site APP cleaving enzyme 1 (BACE1) was attenuated by LBP1C-2, while expression of ADAM10 was up-regulated by LBP1C-2. Moreover, LBP1C-2 promoted the expression of insulin-degradation enzyme (IDE). These results suggested that LBP1C-2 might be a leading compound for anti-Alzheimer’s disease therapy by decreasing Aβ42 production through mediating BACE1 and ADAM10 as well as IDE expression.