Spent pulping chemicals along with liberated lignin called black liquor are a major liquid waste stream from wood digestion process. For wastewater quality improvement, lignin residue could be isolated via various techniques. According to difference in chemical pulping process (kraft and soda), variations of organic and inorganic substance were suspended in waste stream. This research aims to investigate the effects of the cooking chemical on organic waste (lignin) in black liquor. Organic waste in black liquor was isolated as soda lignin (SL) from soda black liquor (SBL) and kraft lignin (KL) from kraft black liquor (KBL) by acidic precipitation. In addition, lignin model compound (LMC) was used to establish base case measurement. The elemental analysis revealed the similarity of C, H, and O content of samples in range of 32-33%, 3-4%, and 35-38%, respectively. FTIR results showed that structures of lignin, functional group and guaiacyl to syringyl ratio were vary depended on type of chemical pulping with β-O-4 as the primary composition of the samples. Moreover, Py-GC/MS technique was applied for analyzing the degradation products in order to corroborate the result with the structure and thermal behavior analysis. The TGA results showed high stability of lignin up to around 400°C. Main degraded compounds of all samples were phenol, vanillin, catechol, and guaiacol. This finding suggested that not only lignin which caused high BOD and COD could potentially be isolated for value added product but also the discharge quality could be improved. In addition, different chemical processes effect residual lignin in black liquor and underscore the importance of lignin in black liquor as a potential material for renewable energy and chemical production.