Hydroxyapatite nanoparticles (HAP NPs) were synthesized by a one‐step hydrothermal method. The surface of HAP NPs was grafted —SH and —COOH chelating groups via in situ surface‐modification with iminodiacetic acid (IDA) and 3‐mercaptopropyl trimethoxysilane (MPS) to afford dual surface‐capped nano‐amendment HAP‐IDA/MPS. The structure of HAP‐IDA/MPS was characterized, and its adsorption performance for Hg²⁺, Cu²⁺, Zn²⁺, Ni²⁺, Co²⁺, and Cd²⁺ was evaluated. The total adsorption capacity of 0.10 g HAP‐IDA/MPS nano‐amendment for Hg²⁺, Cu²⁺, Zn²⁺, Ni²⁺, Co²⁺, and Cd²⁺ with an initial mass concentration of 20 mg·L^-1 reached 13.7 mg·g^-1, about 4.3 times as much as that of HAP. Notably, HAP‐IDA/MPS nano‐amendment displayed the highest immobilization rate for Hg²⁺, possibly because of its chemical reaction with —SH to form sulfide, possessing the lowest solubility product constant among a variety of metal sulfides.