Zinc oxide (ZnO) nanoparticles (nZnO) are among the most commonly used nanoparticles (NPs), and they have been shown to have harmful effects on plants. However, the molecular mechanisms underlying nZnO tolerance and root sensing of NP stresses have not been elucidated. Here, we compared the differential toxic effects of nZnO and Zn2+ toxicity on plants during exposure and recovery using a combination of transcriptomic and physiological analyses. Although both nZnO and Zn2+ inhibited primary root (PR) growth, nZnO had a stronger inhibitory effect on the growth of elongation zones, whereas Zn2+ toxicity had a stronger toxic effect on meristem cells. Timely recovery from stresses is critical for plant survival. Despite the stronger inhibitory effect of nZnO on PR growth, nZnO-exposed plants recovered from stress more rapidly than Zn2+-exposed plants upon transfer to normal conditions, and transcriptome data supported these results. In contrast to Zn2+ toxicity, nZnO induced endocytosis and caused microfilament rearrangement in the epidermal cells of elongation zones, thereby repressing PR growth. nZnO also repressed PR growth by disrupting cell wall organization and structure through both physical interactions and transcriptional regulation. The present study provides new insight into the comprehensive understanding and re-evaluation of NP toxicity in plants.