Currently, nanoparticles are widely used in biomedicine and industry. CuO nanoparticles (CuO-NPs) are versatile materials in our daily life and their toxicity has drawn extensive attention. In this study, we concentrate on the effect of CuO-NPs on early zebrafish development. The results reveal that CuO-NPs can induce abnormal phenotypes of a smaller head and eyes and delayed epiboly. The gene expression pattern shows that CuO-NPs spatially narrow the expression of dorsal genes chordin and goosecoid and alter the expression of dlx3, ntl and hgg which are related to the cell migration of gastrulation. The decreased expression of pax2 and pax6 involved in neural differentiation was accordant with the decreased sizes of neural structures. Cmlc2 expression suggests that CuO-NPs prevented looping of the heart tube during cardiogenesis. Furthermore, quantitative RT-PCR results suggest that the CuO-NPs could increase the canonical Wnt signaling pathway to narrow the expression of chordin and goosecoid in dorsoventral patterning as well as decrease the transcription of Wnt5 and Wnt11 to result in slower, less directed movements and an abnormal cell shape. These findings indicated the CuO-NPs exert developmental toxicity. The present study evaluates the ecological and developmental toxicity, providing warnings about the application of CuO-NPs.