The structure of eucalyptus lignin after ionic liquid (IL) and alkaline ethanol pretreatment processes as well as the influences of this integrated biorefinery on subsequent cellulose hydrolysis were investigated. A maximum yield of 35.0% was achieved for lignin (L-1) prepared from the 1-ally1-3-methylimidazolium chloride pretreated feedstock. The lignins prepared with ILs pretreatment contained lower amount of carbohydrates (0.78-2.13%) than milled wood lignin (MWL, 9.11%) and alkaline ethanol lignin (AEL, 2.29%), and exhibited inhomogeneous molecular weights distribution (M-w, 1395-3050 g/mol) in contrast to MWL(M-w, 2765 g/mol). The lignin preserved basic structure after pretreatment, but had relatively higher amount of beta-O-4' linkages, syringyl units to guaiacyl units (S/G) ratios, and other ending structures. The S/G ratios of lignin increase in the following order: MWL < AEL< L-1, which is in accordance with the increasing amount (Ar/100Ar) of beta-0-4' units of the following lignin fractions: MWL< AEL< L-1. The lignin prepared with ILs pretreatment exhibited a slightly higher thermal stability as compared to MWL, which was probably related to their structural heterogeneity and molecular weights. Additionally, the integrated pretreatment of eucalyptus led to significant improvement of cellulose hydrolysis, and the optimal yield of glucose was 92.6%. (C) 2015 Elsevier Ltd. All rights reserved.