Enzymatic/Mild Acidolysis Lignin (EMAL) was isolated from Cunninghamia lanceolata and eucalyptus woods. The chemical structure and thermochemical properties were characterized by means of elemental analysis, Fourier transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TG), and pyrolysis-gas chromatography combined with mass spectrometry (Py-GC/MS). The EMAL isolated from Cunninghamia lanceolata (C-EMAL) had larger HHV (higher heat value) in comparison to the EMAL isolated from eucalyptus (E-EMAL) due to the greater carbon content of the C-EMAL. The E-EMAL had more syringyl units, whereas the C-EMAL contained more guaiacyl units. It was observed that thermal decomposition occurred over a wide temperature range, and that at a given starting temperature, within the same sample, a higher heating rate produced a higher temperature at which maximum weight loss peaked. The pyrolysis products were mainly composed of carboxylic acids, alcohols, ketones, aldehydes, olefins, alkanes, esters, ethers, and phenols. At all pyrolysis temperatures, the largest components of the pyrolysis products obtained from C-EMAL were the phenols.