Aiming at replacing the noxious solvents commonly employed, ionic liquids (ILs) have been recently explored as novel media for the dissolving of lignin. In the present work, formic acid lignin (FAL) from bamboo and Alcell lignin (AL) from eucalyptus were dissolved in several imidazolium-based ionic liquids, and subsequently regenerated using ethanol–water mixtures and water, respectively. Physiochemical analysis showed major differences in terms of molecular weight, structural transformation, and thermal stability between the original lignin and the regenerated lignin (Re-lignin). The Re-lignin obtained in 1-butyl-3-methylimidazolium chloride ([bmim]Cl) exhibited higher molecular weights than those of Re-lignin obtained in 1-ethyl-3-methylimidazolium acetate ([emim][OAc]) at 120 °C by water regeneration. It was found that up to 46% of the bamboo lignin was dissolved in the [emim][OAc][thin space (1/6-em)]:[thin space (1/6-em)]H2O (5[thin space (1/6-em)]:[thin space (1/6-em)]95 w/w) system at 150 °C. The low value of Mw of Re-lignin (630 g mol−1) was obtained in the [emim][OAc][thin space (1/6-em)]:[thin space (1/6-em)]H2O (50[thin space (1/6-em)]:[thin space (1/6-em)]50 w/w) system, suggesting that the ILs–water system was effective in lignin dissolving and degradation. Measurement of the syringyl to guaiacyl ratio of Re-lignin using HSQC spectra suggested a preferential breakdown of the S unit lignin at high temperature. Nearly the whole amount of β-O-4′ aryl ether linkage of FAL (11.5%) was degraded at 180 °C in [emim][OAc]. The results indicated that the Re-lignin has a higher thermal stability than the corresponding original lignin, which was probably related to their structural heterogeneity and molecular weights.