With the increasing application of ZnO nanomaterials (ZnO‐NMts) in the biomedical field, it is crucial to assess their potential risks to humans and the environment. Therefore, this study aimed to screen for ZnO‐NMts with low toxicity and establish safe exposure limits, and investigate their mechanisms of action. The study synthesized 0D ZnO nanoparticles (ZnO NPs) and 3D ZnO nanoflowers (ZnO Nfs) with different morphologies using a hydrothermal approach for comparative research. The ZnO‐NMts were characterized using X‐ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Mouse brain neuronal cells (NSC‐34) were incubated with ZnO NMts for 6, 12, and 24 h, and the cell morphology was observed using TEM. The toxic effects of ZnO Nfs on NSC‐34 cells were studied using CCK‐8 cell viability detection, reactive oxygen species (ROS) measurement, caspase‐3 activity detection, Annexin V‐FITC/PI apoptosis assay, and mitochondrial membrane potential (Δφm) measurement. The results of the research showed that ZnO‐NMts caused cytoplasmic vacuolization and nuclear pyknosis. After incubating cells with 12.5 µg mL−1 ZnO‐NMts for 12 h, ZnO NRfs exhibited the least toxicity and ROS levels. Additionally, there was a significant increase in caspase‐3 activity, depolarization of mitochondrial membrane potential (Δφm), and the highest rate of early apoptosis.This study successfully identified ZnO NRfs with the lowest toxicity and determined the safe exposure limit to be < 12.5 µg mL−1 (12 h). These findings will contribute to the clinical use of ZnO NRfs with low toxicity and provide a foundation for further research on their potential applications in brain disease treatment.