The integrity of the intestinal mucosal barrier is important for the health of the host. In this study, longan pulp polysaccharides (LP) prevented the intestinal mucosal injury by increasing the expression of mucin 2, tight junction proteins zonulae occludens-1 (ZO-1), claudin-1, claudin-4, and adherens junction E-cadherin in cyclophosphamide-treated mice. To further identify the principle bioactive component of LP, four acidic polysaccharides (LPIa, LPIIa, LPIIIa, and LPIVa) were purified, and their intestinal protection activity in vitro was compared. LPIa, LPIIa, and LPIIIa displayed an ability to increase mRNA expression of ZO-1, claudin-1, occludin, and E-cadherin in differentiated Caco-2 cells, especially LPIa. LPIa has specific structure characteristics: porous surface structure, a high molecular weight (1.47 x 105 Da), and two specific glycosidic linkages of a-Araf-(1 > and 5)-a-Araf-(1. These structure characteristics might primarily contribute to greater intestinal barrier protective effect of LPIa.