Background: Lignin is an abundant natural polymer obtained as a by-product from the fractionation of lignocellulosic biomass. In the name of a circular economy, lignin should be valorised into valuable chemicals or biomaterials and utilised instead of petrochemicals. For the development of efficient valorisation processes, the structural characterisation of lignin can be highly beneficial. However, this is an arduous task, as the isolated (and sometimes processed) lignin mainly consists of various neutral monomers but also oligomers. In addition, the material contains isomers, which can be especially problematic to separate and identify. Results: We present a powerful off-line comprehensive two-dimensional (2D) chromatography method combining liquid chromatography (LC), supercritical fluid chromatography (SFC), and high-resolution mass spectrometry for the non-target analysis of depolymerised lignin. The implementation of a 1-aminoanthracene column in the second dimension enabled a class separation of potential lignin monomers, dimers, trimers, and tetramers with an additional separation based on the number of hydroxyl groups and steric effects. The pentafluorophenyl column in the first dimension additionally improved the separation based on hydrophobicity. The comparison of off-line 2D LC×SFC to 1D SFC showed that besides the overall improved performance, the first method is also superior for the separation of isomers. Advanced data analysis methods (MS-DIAL, SIRIUS, and Feature-Based Molecular Network) were integrated into the non-target workflow to rapidly visualise and study the detected compounds, which proved to be especially beneficial for the characterisation of the separated isomers. Significance: The method yielded the first 2D LC plot demonstrating a classification of lignin compounds, which can be applied to compare various lignin sources and processing methods. In addition, the technique demonstrated improved separation of compounds, including isomers, which was especially beneficial as 77% of the detected compounds had at least one isomer in the same lignin sample.