The purpose of this study was to evaluate the effects of β-conglycinin on intestinal permeability, intestinal morphology and the expression of tight junction protein in Rhynchocypris lagowski Dybowski. 750 Rhynchocypris lagowski Dybowski (4.61 ± 0.01 g) were divided into 5 groups (CK, β-20, β-40, β-60 and β-80 groups) and fed with 5 diets contained, respectively (0, 20, 40, 60 and 80 g/kg), β-conglycinin for 8 weeks. These results showed dietary β-conglycinin could destroy the structural integrity of intestine, cause villus to break and shrink, and the epithelium and lamina propria to separate. Simultaneously, compared with CK group, the levels of Diamine oxidase (DAO), 5-Hydroxytryptamine (5-HT), D-lactic acid (D-LA) and Endothelin-1 (ET-1) in serum were significantly increased in β-20, β-40, β-60 and β-80 groups (P < .05). In proximal intestines (PI), the expression of Zonula occludens-1 (ZO-1) and Occludin-b was significantly reduced, and lamina propria width was significantly increased in β-60 and β-80 groups (P < .05), and fold height, muscular layer thickness and the expression of Claudin were significantly decreased in β-40, β-60 and β-80 groups (P < .05), and the expression of Occludin-a was significantly decreased in β-20, β-40, β-60 and β-80 groups (P < .05); in addition, the expression of ZO-1 in PI was significantly increased in β-20 and β-40 groups (P < .05). In mid intestines (MI), fold height and the expression of ZO-1 and Claudin were significantly reduced, and lamina propria width was significantly increased in β-40, β-60 and β-80 groups (P < .05), and the expression of ZO-1 was significantly increased in β-20 groups (P < .05), and muscular layer thickness and the expression of Occludin-a and Occludin-b were significantly decreased in β-20, β-40, β-60 and β-80 groups (P < .05). In distal intestines (DI), fold height and the expression of ZO-1, Claudin, Occludin-a and Occludin-b were significantly reduced, and lamina propria width was significantly increased in β-20, β-40, β-60 and β-80 groups (P < .05), and muscular layer thickness was significantly reduced in β-40, β-60 and β-80 groups (P < .05). In summary, dietary β-conglycinin had negative effects on tight junctions, intestinal permeability and morphology. Moreover, the negative effects of β-conglycinin on intestines from high to low were DI, MI and PI in our study.