Soda process is one of the most important pulping processes in paper industry producing large quantities of alkali lignins that can afford plenty of biofuels, aromatic chemicals and materials. However, the structural and size-related heterogeneities and complexities hinder the development in these directions. Herein, we report new insights into the structure of alkali lignin, through investigating the formation and transformation of enol ether and arylglycerol structures that are significant responsible for the structural transformation from native lignin to alkali lignin. Four-type enol ethers composed of G/S units in hardwood alkali lignin were identified by 2D HSQC NMR. A series of alkali lignins prepared by alkali treatment of eucalyptus cellulolytic enzyme lignin under various temperatures were analyzed by 2D HSQC NMR, 31P NMR and gel permeation chromatography (GPC). Upon these analyses and related model compound studies, it was found that the arylglycerols formed from native β-O-4 linkages tends to be oxidized with the further degradation of aryl ether bonds, and that the enol ether linkages are facile to be hydrolyzed or oxidized in the air. These insights improve the mechanistic understanding for the structural evolution and the diversity of alkali lignins and will aid the development of further lignin valorization strategies.