Bisphenol A (BPA) and di-n-butyl phthalate (DBP) are well-known endocrine-disrupting chemicals (EDCs) that have human health risks. Chronic exposure to BPA and DBP increases the occurrence of human disease. Despite the potential for exposure in embryonic development, the mechanism of action of BPA and DBP on vertebrate development and disease still remains unclear. In the present study, we identified proteins and protein networks that are perturbed by BPA and DBP during zebrafish (Danio rerio) development. Zebrafish embryos were exposed to environmentally relevant levels of BPA (10 μg/L) and DBP (50 μg/L) for 96 h. By iTRAQ labeling quantitative proteomics, a set of 26 and 41 differentially expressed proteins were identified in BPA- and DBP-treated zebrafish embryos, respectively. Integrated toxicity analysis predicted that these proteins function in common regulatory networks that are significantly associated with developmental and metabolic disorders. Exposure to low concentrations of BPA and DBP has potential health risks in zebrafish embryos. Our results also show that BPA and DBP significantly up-regulate the expression levels of multiple network proteins, providing valuable information about the molecular actions of BPA and DBP on the developmental systems.