Alkylphenolic endocrine disruptors (Eds) have been known to affect development of the descendants of multipotent neural crest cells (NCCs) in amphibian embryos. To unravel the mechanism of head dysgenesis induced by alkylphenols in amphibians, the effect of 4-octylphenol (OP) on the differentiation of cranial NCCs in developing embryos and tadpoles, ex vivo NC explant, and isolated NCCs was examined in fire-bellied toad Bombina orientalis with 0, 1, 2, 5, 10, 25 and 50 μM concentrations. Following OP treatment, head cartilages were frequently absent together with the decreased col2a1 mRNA level in tadpoles. While the lipid hydroperoxide (LPO), endoplasmic reticulum stress (ERS), apoptosis, and DNA fragmentation were significantly increased in stage 22 neulurae and heads of stage 45 tadpoles. In stage 22 neulurae, OP decreased sox9 mRNA, the master transcription factor for chondrogenic differentiation and increased undifferentiated NCC markers. The ectopic NCCs were found in endoderm while mesodermal SOX10(+) cells were decreased. In cranial NCCs isolated from stage 22 embryos, OP treatment decreased cellular survival and increased apoptosis, epithelial-mesenchymal transition (EMT) and cell migration. In chondrogenic induced cranial NC explants, OP treatment decreased SOX9(+) chondrocytes and cartilage development. Together, OP potentiated oxidative damage, apoptosis, EMT, and ectopic migration of NCCs. Considering that tissue differentiation requires stem cells to activate the molecular mechanism of differentiation at the correct location during embryonic development, these changes caused by OP may inhibit sox9-dependent chondrogenic differentiation of cranial NCCs, leading to head dysgenesis in B. orientalis embryos. Therefore, developing multipotent NCCs could be an important target of OP, provides new direction for the estimation of the risk of EDs exposure in human and wildlife animals.