A catalytic method for the isolation of lignin in high purity from cotton stalk was presented in this study. Lignin fractions were obtained by the extraction of cotton stalk under catalytic hydrothermal conditions in the presence of metal chlorides including AlCl3, CrCl3, FeCl3 and ZnCl2 as catalysts. Structural elucidation of these lignin samples was investigated by high-performance anion-exchange chromatography (HPAEC), gel permeation chromatography (GPC), and 2D HSQC NMR spectroscopy. The results showed that the separated lignin fractions possessed higher purities than milled wood lignin (MWL). 2D NMR spectra demonstrated that guaiacyl (G) and syringyl (S) units were predominant in these lignin fractions, similar to the typical lignin types of hardwood. Moreover, the obtained lignin fractions consisted mainly of β-O-4′ aryl ether linkages, followed by resinol and phenylcoumaran structures. It was also found that the cleavages of β-O-4′ linkages occurred remarkably due to the presence of catalysts, and their decreasing severities were consistent with the acidity of the metal chlorides. In addition, the degradation was accompanied by a mild repolymerization during the catalytic hydrothermal pretreatment. In consideration of the relatively high yield and purity, isolation of lignin from raw materials by using catalytic hydrothermal pretreatment catalyzed by AlCl3 provided us a more effective approach for biomass pretreatment.