Uncovering the structure of lignin from biorefinery has an important effect on lignin catalytic depolymerization and the production of bioenergy. In this study, two biorefinery lignins were isolated from tobacco stalks via alkaline and deep eutectic solvent (DES) catalyzed delignification processes, and the lignin heterogeneity structural characteristics were elucidated by gel permeation chromatography, 2D-HSQC, FT-IR, etc., to understand the relationship between the structure and the thermal characteristics of lignin. It was found that the lignins presented various structural characteristics and components, in which the predominant interunit linkages of black liquor lignin are β-O-4 and β-β linkages, and the β-O-4 linkages disappeared by DES treatment. DES lignins exhibited lower molecular weights and yields than black liquor lignin. Thermogravimetric analysis and fixed-bed pyrolysis were also performed to investigate the lignin thermal behavior. The results show that the DES approach can improve the bio-oil production from lignin and highlight the potential of DES lignin as a promising feedstock in the lignin pyrolysis process. This work provides a valuable example of the conversion of biorefinery lignin into pyrolysis products.