Nonylphenol (NP) is the environmental endocrine disruptor that widely presents in water, which affects the growth and development of species. In order to explore the mechanism of nonylphenol-induced developmental malformation in red crucian carp (Carassius auratus red var.), red crucian carp was used as the research model, transcriptome sequencing (RNA-seq) of normal embryos in neural stage (NC), normal embryos in 21 somite stage (SC), monstrous embryos in neural stage and monstrous embryos in 21 somite stage that exposed to 5 μmol/L NP (SNP) were performed on Illumina HiSep 2500 platform. Furthermore, differentially expressed genes (DEGs) were verified by quantitative real-time PCR (qRT-PCR). A total of 89,166 high-quality Unigenes were obtained from RNA-seq, of which 30,319 Unigenes were annotated. Pairwise comparison among NC, SC, NNP and SNP showed that there were 153 DEGs in NC/NNP, 10 DEGs in SC/SNP, 6121 DEGs in NC/SC, and 7270 DEGs in NNP/SCP. KEGG pathway analysis revealed that most of these above DEGs were enriched to cellular processes, environmental information processing and metabolism signal pathways. 25 DEGs related to growth, development, cytoskeleton and cardiovascular circulation were verified by qRT-PCR. Their expression changes are consistent in qRT-PCR and RNA-seq. On the one hand, this consistency indicates that the RNA-seq results are reliable, on the other hand, the candidate genes of developmental malformation caused by NP stress are preliminarily excavated, which provides prophase data for further study on the molecular mechanism of NP teratogenesis.