Sugarcane bagasse was pretreated with atmospheric glycerol organosolv (AGO) and alkaline-catalyzed atmospheric glycerol organosolv (al-AGO) process, respectively. Then, their individual lignin, AGO lignin (AGOL) and al-AGO lignin (al-AGOL), was obtained by using acid precipitation method from the pretreatment liquor. With a single-factor and orthogonal experiment, the lignin extraction condition was optimized as follows: centrifugation speed 8000r/min, centrifugation time 15min, pH=3, glycerol solution concentration 10%. Under optimized condition, the extraction of AGOL and al-AGOL reached 72% and 76%, respectively. Scanning electron microscopy (SEM), elemental analysis, ultraviolet spectroscopy (UV), gel permeation chromatography (GPC), 1H nuclear magnetic resonance spectroscopy and thermogravimetric analysis were used to characterize the structure of extracted lignin. Additionally, the antioxidant activity of these lignin samples was measured. Results showed that three types of lignin, milled bagasse lignin(MBL), AGOL and al-AGOL extracted from sugarcane bagasse predominantly presented a spherical morphology of particles. Compared with MBL, the AGOL and al-AGOL showed smaller molecular weight, narrower distribution, better uniformity, higher thermal stability and antioxidant activity, which are of good promise for using as important industrial raw materials.