The synchronous removal of toxic heavy metals (e.g., cadmium (Cd), lead (Pb), and etc.) from the contaminated water environment is an urgent demand in the pollution control field. Herein, an innovative adsorbent synthesis idea was proposed and a series of cysteine-functionalized nanohydroxyapatite (CysHAP) composites were prepared by adopting different reaction temperatures, cysteine/HAP ratios, and synthesis methods. According to the single factor tests, a co-precipitation temperature of 25 °C with a molar cysteine/HAP ratio of 2.0 was selected to synthesize the optimum CysHAP2.0–25 composite. Multiple characterization results showed that cysteine markedly altered the morphology, crystallinity, and crystal structure of HAP, leading to the formation of CysHAP2.0–25 composite with a superior dispersity, a smaller crystal size, a higher specific surface area, and a greater number of binding sites. Compared with HAP-25, the CysHAP2.0–25 composite exhibited a better Cd(II) sorption performance and a 100% Pb(II) removal in a wide range of solution pH and background electrolyte concentration. The removal performance of CysHAP2.0–25 composite towards Cd(II) was suppressed by the coexisting aqueous components with an obviously stronger inhibiting action of humic acid (HA) than low molecular weight organic acids (LMWOAs) and mixed inorganic components (IC). Pb(II) slightly reduced the sorption ratio of Cd(II) and forced Cd(II) to bind on the -SOx sites derived from sulfhydryl oxidation. In contrast, Cd(II) had no impact on the sorption behaviors of Pb(II). Overall, the synthesized CysHAP2.0–25 composite could be potential applied for the purification of Cd- and Pb-bearing water systems.