Objective The effects of zirconium dioxide nanoparticles (ZrO₂-NPs) exposure on the histone H3 modification in human skin keratinocytes (HaCaT) were clarified, and the underlying mechanism of histone H3 modification changes was explored in this study to provide a theoretical basis for the further safe application of nanomaterials.Methods The ZrO₂-NPs were firstly characterized in detail by means of scanning electron microscope, laser particle size analyzer, X-rad diffraction, etc. Subsequently, the effects of ZrO₂-NPs exposure on the cell viability, intracellular accumulation and histone H3 modification were evaluated by Western blotting and flow cytometry.Results The results showed that ZrO₂-NPs after dispersion treatment exhibited obvious agglomeration, and their specific surface area decreased whereas the secondary particle size increased. The phosphorylation of histone H3 at serine 10, the acetylation of histone H3 at lysine 9 and 14, the trimethylation of histone H3 at lysine 4 and 27 were induced to upregulate by ZrO₂-NPs in a short time (1 h). Through further analysis, it was found that the intracellular accumulation of ZrO₂-NPs and the level of DNA damage caused by ZrO₂-NPs were linearly correlated with the level of histone H3 modification induced by ZrO₂-NPs.Conclusion These results suggested that the changes of the common modification sites of histone H3 in HaCaT cells were induced after exposure of ZrO₂-NPs. The intracellular accumulation of ZrO₂-NPs is one of the key factors in its induction of changes in histone H3 modification, and regulation mechanism of histone H3 modification may be involved in DNA damage repair pathways.