Soybean agglutinin (SBA) is a main anti-nutritional factor in soybean. SBA exhibits its anti-nutritional functions by binding to intestinal epithelial cells. Keratin8 (KRT8), Keratin18 (KRT18) and Actin (ACTA) are the representative SBA-specific binding proteins. Such cytoskeletal proteins act a crucial role in different cell activities. However, there are limited reports revealing what the signal transduction pathway of apoptosis caused by SBA when binding to KRT8, KRT18, ACTA. We aimed to evaluate the effects of SBA on cell apoptosis and the expression of the cytoskeletal protein (KRT8, KRT18, ACTA), to reveal the roles of these cytoskeletal proteins or combinations of them on SBA-induced cell apoptosis in IPEC-J2 cell line, to evaluate the influences of SBA on the mitochondria, endoplasmic reticulum stress and death receptor mediated apoptosis signal pathway; and to show the roles of KRT8, KRT18 and ACTA in different apoptosis signal pathways induced by SBA. The results showed that SBA induced the IPEC-J2 cell apoptosis and decreased the mRNA expression of KRT8, KRT18 and ACTA (p < 0.05). The degree of effect of three cytoskeleton proteins on cell apoptosis was ACTA > KRT8 > KRT18. The roles of these three cytoskeletal proteins on IPEC-J2 apoptotic rates had a certain accumulation effect. SBA up-regulated mitochondrial fission variant protein (FIS1) and fusion protein (Mfn2), promoted CytC and AIF in mitochondria to enter the cytoplasm, activated caspase-9 and caspase-3, damaged or declined mitochondrial function, and reduced ATP synthesis (p < 0.05). SBA also up-regulated the expression of GRP78, XBP-1, eIF2α, and CHOP (p < 0.05), down regulated the expression level of ASK1 protein (p < 0.05). SBA led to recruitment of FADD to the cytoplasmic membrane, increased the expression of FasL, resulting in caspase-8 processing. SBA up-regulated the expression level of Bax protein, and decreased cytosolic Bcl-2 and Bid (p < 0.05). In addition, there was a significant negative correlation between the gene expression of cytoskeleton proteins and apoptosis, as well as the expression of key proteins of apoptosis related signal transduction pathways. In conclusion, SBA induced the activation of the mitochondria, endoplasmic reticulum stress and the death receptor mediated apoptosis signal pathway and the crosstalk between them. The effect of SBA on these three pathways was mainly exhibited via down regulation of the mRNA expression of the three cytoskeletal expressions. This study elucidates the molecular mechanism and signaling pathway of SBA led to apoptosis from the perspective of cell biology and molecular biology, and provides a new perspective on the toxicity mechanism of other food derived anti nutrients, medical gastrointestinal health and related cancer treatment.