Lignin is a promising raw material for membrane fabrication due to its abundant oxygen-containing functional groups, branched molecular structure, and high abundance in the botanic field. In this report, polydopamine (PDA) coated carbon nanotubes (PCNTs) are synthesized. Then, a PCNT-incorporated lignin-based loose nanofiltration membrane is fabricated using quaternized lignin (QL) as a raw material, triphosgene (TP) as a crosslinker, and PCNTs as nanoadditive by interfacial polymerization. The results show that the PCNTs uniformly distribute in the QL-based separation layer providing quick diffusion paths for water molecules and salt ions. The coated PDA layer improves the chemical compatibility between the PCNTs and the separation layer. The incorporated PCNTs optimize the membrane microstructure and elevate the pure water permeance to 45.5 LMH bar−1. The membrane exhibits high rejections to various dyes (> 90%) and high salt permeation (> 90%), demonstrating an excellent dye/salt separation performance. Moreover, it has satisfactory capabilities for resisting dye adsorption and fouling, and its separation capability also has good tolerances to the acid, alkali, and active chlorine treatments. The quaternary ammonium ions and hydrophilic surface endow the membrane with favorable bactericidal property (99.3%) and bacteria-adhesion resistance. Besides, TP is a better crosslinker than trimesoyl chloride for optimizing the membrane microstructure and crosslinking degree in terms of dye/salt separation.