3C syndrome features craniofacial, nervous, and cardiovascular malformations. WASHC5 gene mutations may underline this syndrome, but the pathogenicity and underlying mechanism remain undetermined. We analyzed the expression pattern of the washc5 gene in zebrafish using whole-body in situ hybridization and generated a zebrafish model with washc5 gene knockout using CRISPR/Cas9 technology. Homozygous zebrafish exhibited high mortality, retarded growth, lighter stripes, and reduced pigmentation around the pupils. In the maxillofacial region, homozygotes displayed a shortened and tilted maxilla and delayed ossification of bones. In the heart, homozygous zebrafish showed a decreased heart rate, increased ventricular area, disorganized ventricular muscle fibers, mitochondrial swelling, Golgi lysis, and endoplasmic reticulum (ER) lysis in ventricular myocytes. The mRNA levels of nppb and myh7 were significantly increased. In the nervous system, homozygotes displayed bradykinesia and impaired neuronal development. qRT-PCR analysis revealed downregulation of col1a2, col1a1a, col1a1b, sp7, and msx2b (osteogenic factors and regulators of maxillofacial skeletal development) and abnormal expression of alpk2, alpk3b, actc2 (cardiac development factors), as well as tsen54, exosc8, and exosc9 (cerebellar development factors). Enrichment analysis of differentially expressed genes and proteins indicated involvement in ER-related processes. The washc5 knockout zebrafish model exhibits phenotypic similarities to human 3C syndrome, suggesting that mutations of this gene may play a pathogenic role in the syndrome. The mechanism of the washc5 gene in 3C syndrome may be associated with disturbances in ER homeostasis, providing insights into potential gene therapy strategies.