Dissolved lignin in eucalyptus black liquor was obtained at five different reaction times (1 h to 5 h) throughout the main delignification process to reveal the structural changes of lignin and its contributions to pollution load at different degrees of delignification. During the delignification process, the lignin removal efficiency and Kappa number of the pulp had a clear linear relationship with the holding time at the highest temperature (170 C). This indicated that the degree of delignification to which the pulp could be regulated by the holding time. Condensation and degradation appeared to participate as two competitive reactions in the cooking process. The condensation structures of lignin increased remarkably in the first 3 h, which resulted in increased molecular weight. Then, the degradation of lignin became the main reaction at longer reaction times (4 h to 5 h), when the β-O-4’ and β–β’ bonds were dramatically broken. Furthermore, the lignin concentration in black liquor increased with delignification time, which had a positive correlation to chemical oxygen demand (CODcr) in black liquor. The proportion of CODcr produced by lignin increased remarkably in the decomposition stage of lignin, which revealed the importance of changes in the lignin structure during the delignification process to the pollution load.