The LCC fractionation process developed by us has been further rationalized and successively applied for flax Soda-AQ pulps in demonstrating its universal applicability on all types of wood and non-wood species. The LCC characterization results revealed that native lignin is substantially attached at hemicelluloses, as xylan-lignin (accounted for 49% over the total amount of wood Klason lignin in eucalyptus and 20% in spruce) or as glucomannan-lignin (53% in spruce wood). As an example of adventive (manipulated) LCC structure, phenolic mediator-coupled xylan structure was identified at the xylan-lignin fraction prepared from laccase-mediator treated flax Soda-AQ pulps. The coupling took place between the mediator, lauryl gallate, and hexenuronic acid (HexA) at the intermediate layer in the pulps.