In this work, the effects of β-nucleating agent and annealing treatment on the crystallization and amorphous phase in impact polypropylene copolymer (IPC) were profoundly displayed to reveal the toughening mechanism of the modified product. The toughness of β-nucleated IPC was improved dramatically compared with samples without nucleation agent. The chain mobility measured by dynamic mechanical analysis (DMA) in the rigid amorphous fraction (RAF) weakened with increasing annealing temperature, while that in the mobile amorphous fraction (MAF) strengthened under low annealing temperatures (not more than 124 °C) and then weakened at higher temperatures. On the one hand, the impact energy is effectively dissipated by slipping of loose β lamellae. On the other hand, the voids in loose β crystals multiply shear yielding. By contrast, dense α crystals in neat IPCs provide fewer voids and the major pathway of energy dissipation is crazing induced by soft dispersed particles. After annealing treatment, all the β-nucleated IPCs became brittle, which was mainly ascribed to the reduction of β crystals through β–α transformation.