Removal behavior of organic pollutants such as lignin in cotton pulp black liquor (CPBL) was investigated in precipitation followed by electrochemical oxidation (EO) using FeCl3, Fe2(SO4)3, FeCl2 and FeSO4 as precipitants, electrolyte and catalysts. Based on comparison of precipitation efficacy of iron salts, spectroscopic techniques, thermodynamic equilibrium calculations and molecular dynamics (MD) simulations were used to provide insight into the interaction between iron cations and lignin. The results showed that FeCl3 achieved the highest removal of chemical oxygen demand (COD, 76.05%), UV254 (69.21%) and lignin (78.28%). Iron cationic complexation with lignin was identified as the key mechanism in precipitation. Fe3+ was more active in binding to organic ligands mainly due to charge effect compared to Fe2+. The strong Fe−sulphate coordination affected the complexation with lignin. MD simulations showed the formation of inner sphere complexes of iron cations with deprotonated carboxyl and hydroxyl groups via bidentate and monodentate coordination. The removal efficiency of electrochemical oxidation (EO) as a post−treatment of the precipitation was dependent on iron salts. Removals of COD, UV254 and color can achieve 98.88%, 98.9% and 99.97% by FeCl3 precipitation and EO processes. The effluent reached the primary discharge standard specified in Integrated Wastewater Discharge Standard of China (GB8978−1996). FeCl3 demonstrated significant advantages in the removal of organic pollutants from cotton pulp black liquor in the combined process of precipitation and electrochemical treatment and may have practical application potential.