CuO nanoparticles (NPs) (20, 50 mg L–1) inhibited seedling growth of different Arabidopsis thaliana ecotypes (Col-0, Bay-0, and Ws-2), as well as the germination of their pollens and harvested seeds. For most of growth parameters (e.g., biomass, relative growth rate, root morphology change), Col-0 was the more sensitive ecotype to CuO NPs compared to Bay-0 and Ws-2. Equivalent Cu2+ ions and CuO bulk particles had no effect on Arabidopsis growth. After CuO NPs (50 mg L–1) exposure, Cu was detected in the roots, leaves, flowers and harvested seeds of Arabidopsis, and its contents were significantly higher than that in CuO bulk particles (50 mg L–1) and Cu2+ ions (0.15 mg L–1) treatments. Based on X-ray absorption near-edge spectroscopy analysis (XANES), Cu in the harvested seeds was confirmed as being mainly in the form of CuO (88.8%), which is the first observation on the presence of CuO NPs in the plant progeny. Moreover, after CuO NPs exposure, two differentially expressed genes (C-1 and C-3) that regulated root growth and reactive oxygen species generation were identified, which correlated well with the physiological root inhibition and oxidative stress data. This current study provides direct evidence for the negative effects of CuO NPs on Arabidopsis, including accumulation and parent-progeny transfer of the particles, which may have significant implications with regard to the risk of NPs to food safety and security.