Nanomaterials may have effects on health and environmental safety due to their unique physical and chemical properties. Nanometer hydroxyapatite (NHAP) is a commonly used passivator for fixing heavy metals in soil and remediating soil pollution. We evaluated the phytotoxicity of NHAP, its effects on the sprouting of plants, and the growth of root tip border cells by measuring the effects of NHAP on the germination rate of cucumber and the number and activity of root border cells in indoor cultivation and hanging cultivation by flow cytometry. The germination percentage and germination index of cucumber increased rapidly with increasing concentration of NHAP. When the concentration was greater than 1000 mg L⁻¹, both root growth and shoot growth were inhibited to varying degrees. The highest number and activity of root border cells were observed during germination of cucumber seeds at a root length of 20 mm. Cell survival decreased steadily with increasing root growth, reaching the lowest survival rate of 55.4% at 40 cm. Decrease in the number of root border cells was observed following treatment with NHAP, with the rapid decreases observed at NHAP concentrations greater than 500 mg L⁻¹. This result demonstrates that a high concentration of NHAP exerts a harmful or inhibitory effect on the growth of cucumber root. Pectin methylesterase (PME) activity increased with increasing NHAP concentration, therefore protecting the plant from the increased entry of metal ions into the cells.