Molecular iodine has been introduced into the alkali lignin (AL) solutions to adjust the pi-pi aggregation, and the effect of lignin-iodine complexes on the aggregation and assembly characteristics of AL have been investigated by using fluorescence, UV-vis spectroscopy, light scattering, and viscometric techniques. Results show that AL form pi-pi aggregates (i.e., J-aggregates) in THF driven by the pi-pi interaction of the aromatic groups in AL, and the pi-pi aggregates undergo disaggregation in THF-I-2 media because of the formation of lignin-iodine charge-transfer complexes. By using iodine as a probe to investigate the aggregation behaviors and assembly characteristics, it is estimated that about 18 mol % aromatic groups of AL form pi-pi aggregates in AL molecular aggregates. When molecular iodine is introduced into the AL solutions, lignin-iodine complexes occur with charge-transfer transition from HOMO of the aromatic groups of AL to the LUMO of iodine. The formation of lignin-iodine complexes reduces the affinity of the aromatic groups approaching each other due to the electrostatic repulsion and then eliminates the pi-pi interaction of the aromatic groups. The disaggregation of the pi-pi aggregates brings a dissociation behavior of AL chains and a pronounced molecular expansion. This dissociation behavior and molecular expansion of AL in the dipping solutions induce a decrease in the adsorbed amount and an increase in the adsorption rate, when AL is transferred from the dipping solution to the self-assembled adsorbed films. Consequently, the adsorption behavior of AL can be controlled by adjusting the pi-pi aggregation. Above observations give insight into the occurrence of J-aggregation of the aromatic groups in the AL molecular aggregates and the disaggregation mechanism of AL aggregates induced by the lignin-iodine complexes for the first time. The understanding can provide an academic instruction in the efficient utilization of the alkali lignin from the waste liquor and also leads to further development in expanding functionalities of the aromatic compounds through manipulation of the pi-pi aggregation.