Heavy metals have raised an increasing number of pollution incidents and resulted in potent damages to aquatic ecosystems and human health. Thus, effective and efficient approaches to eliminate heavy metal ions are in urgent needs. Herein, novel hybrid nanoparticles have been prepared by a facile method using epichlorohydrin as a cross-linker between amino-functionalized magnetic nanoparticles and carboxymethylated lignin. Multiple characterization methods including XRD, FTIR, XPS, SEM, and TEM confirmed the formed nanostructures and the chemical features of the lignin-based hybrid nanoparticles. The as-synthesized hybrid nanoparticles exhibited high adsorption capacities of 150.33 and 70.69 mg/g for Pb2+ and Cu2+, respectively. More importantly, the adsorption equilibriums of Pb2+ and Cu2+ onto hybrid nanoparticles can be achieved within 30 s, which are among the fastest functional adsorbents for Pb2+ and Cu2+ removal as reported by now. The ultrafast adsorption is ascribed not only to the nanostructures, but also to the abundant active sites provided by the carboxymethylated lignin. The mechanism of removing Pb2+ and Cu2+ by hybrid nanoparticles could be mainly attributed to ion exchange and hydrogen bonding. The tailored nanostructured hybrid nanoparticles with exceptional adsorption effectiveness and efficiency are low-cost and eco-friendly, which potentially meets the cost-effective criteria for producing the water treatment adsorbents on a large scale.