This study focused on the structural differences of lignin after pyridine–acetic acid–water (PAW) and dioxane–acidic water (DAW) purification processes. These structural differences included the S/G ratio, condensed structure, weight-average (MW) molecular weights, β-O-4 linkages and sugar content. The chemical structure of the isolated crude lignin (CL), PAW purified lignin (PPL) and DAW purified lignin (DPL) was elucidated using quantitative 13C NMR, 2D-HSQC NMR spectra, thermogravimetric analysis (TGA), gel permeation chromatography (GPC) and Fourier transform infrared spectroscopy (FTIR). The results showed that the PPL fractions contain fewer condensed structures, higher S/G ratios, more β-O-4 linkages, higher average MW and lower thermal degradation properties compared to the CL and DPL fractions. Furthermore, the PAW process was more selective in removing condensed units and enriching S-type lignin from CL compared to the DAW process. These results provide valuable information for understanding which purification process is more suitable to be applied for lignin.