The chemical compositions of cotton stalk and bast are similar to those of hardwood and superior to those of grass fiber. With respect to the morphological characteristics of their fibers, cotton stalk is similar to hardwood and cotton bast is similar to softwood. The average length of cotton bast fibers is nearly triple that of cotton stalk fibers, and the length-to-width ratio is almost quadruple. Traditionally, cotton stalk and cotton bast are pulped together, which affects the quality and homogeneity of the pulp and complicates bleaching, limiting its use to low-grade paper. In this study, cotton bast and cotton stalk were separated and pulped individually by alkaline peroxide extrusion pulping (APEP). The orthogonal analytical method was used to determine the optimal pulping parameters. Compared to those obtained via the kraft pulp (KP) of cotton stalk as a whole, far superior yield and whiteness were obtained in APEP. Further, with APEP, lower amounts of chemicals and less energy were consumed and there was little pollution. The physical performance of APEP was slightly lower than that of KP. With respect to bast alone, the physical performance of APEP was almost as good as that of KP.