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A novel fabrication method for modifying alkaline lignin (AL) was reported, in which trimercapto-s-triazine trisodium salt was used as a modifier to tune surface properties of AL. Molecular structure of modified AL (FAL) was determined by 3D-EEM, synchronous fluorescence, FTIR, 13C MAS NMR and XPS. Two-dimensional correlation spectroscopy and electron localization function demonstrated that both of electrostatic and coordinate bonds formed between these functional groups and Pb(II) at higher pH of 3.0 to 6.0 while only coordinate bond at lower pH of 0.2 to 1.2. The higher the solution pH was, the stronger the adsorption capacity of FAL had. The maximum adsorption capacity (qm) of Pb(II) was 20.0, 28.2, 65.1 and 73.7 mg/g at pH of 0.2, 1.2, 3.0 and 6.0 (T = 25 °C), respectively. The adsorption performance of FAL towards Pb(II) was better by comparing with other biomass-based materials via adsorption amount, equilibrium time as well as simplicity of the synthesized steps. These results improve the understanding of FAL-Pb(II) interaction at the molecular level and facilitate a comprehensive evaluation on the treatment efficiency of FAL.