Nanohydroxyapatite (n-HAP) as an environmentally friendly adsorbent of heavy metal ions still requires the rational design of the pore structure and surface characteristic for enhancing their adsorption capacity toward heavy metal ions. A novel one-step strategy was developed to regulate the pore structure and surface characteristic of esterified HAP (n-EHAP) nanocrystals (NCs) for enhancing the adsorption capacity by incorporation of 2-bromo-2-methylpropionate (2-BrMP) groups on the surface of n-EHAP NCs. When using water as the sole solvent, the aggregation of n-EHAP NCs became unavoidable because of incorporation of hydrophobic 2-BrMP groups on n-HAP particle surfaces. The synthesis of uniform and individual n-EHAP NCs was achieved by rational adjustment of the aqueous dispersion medium to avoid agglomeration and precipitation, which was induced by the changing surface characteristic of n-EHAP NCs during the continuing incorporation of hydrophobic 2-BrMP groups in the water/acetone system. The successful incorporation of hydrophobic 2-BrMP groups on the surface of n-EHAP NCs was characterized by X-ray powder diffraction, field-emission scanning electron microscopy, transmission electron microscopy, Fourier transform infrared spectroscopy, and liquid nitrogen adsorption isotherms. To explore the potential application in water treatment, a series of systematically designed batch experiments were conducted to determine the influences of the adsorbent dosage, solution pH, and contact time on the adsorption behavior of n-EHAP NCs. Experimental results indicated that the addition of water-soluble acetone greatly promoted the formation of individual n-EHAP NCs without aggregation, and furthermore, the successful incorporation of hydrophobic 2-BrMP groups led to formation of porously structured n-EHAP NCs with a higher surface area and an increasing micro-/mesopore ratio. Compared with pristine n-HAP, n-EHAP NCs exhibited lower crystallinity with smaller crystallite size and demonstrated an ultrahigh adsorption capacity for Pb(II) in acidic solution with a record of close to 2400 mg/g. The improved performance of n-EHAP NCs originated from both the suitable porous structure with a higher micro-/mesoporosity ratio and the existing tethered 2-BrMP group-induced the ester bond, providing more adsorption active affinity sites for heavy metal ions. The highly efficient adsorption (99.99%) was further achieved using tap water spiked with traces of Pb(II) (63 ppb). The presented findings promise the application of n-EHAP NCs in water treatment as an alternative, low-cost, and ecofriendly adsorbent for environmental remediation.