The elucidation of the structures of individual lignin molecules in heterogeneous lignin isolates poses a challenge, underscoring the need for the development of robust analytical methods. Herein, we report the combined use of NMR and MALDI-TOF MSn as a facile approach for distinguishing and determining the detailed structures of individual oligomeric molecules in heterogeneous lignin mixtures. Supported by NMR, MALDI-TOF analysis of acetylated lignins provides precision by enabling the facile discernment of inter-unit linkages in lignin molecules. Furthermore, the progression of lignin linkages could be tracked through population studies, yielding a structural progression map that elucidates the chemical features of individual oligomers in milled wood lignins and synthetic lignins. By unmasking lignin’s molecular heterogeneity, this study marks an essential milestone in lignin analytics with possibility to advance the frontiers of molecular-level research in both fundamental and applied lignin studies.