Lightweight materials with high strength and long cyclic lifespan are greatly demanded in practical applications, yet these properties are usually mutually exclusive. Here, we present a strong, lightweight, highly deformation-tolerant, and fatigue-resistant carbon nanotube (CNT) composite enabled by an amorphous/crystalline heterophase carbon shell. In particular, we obtain nanocrystallites with CNT-induced crystalline orientation uniformly embedded within an amorphous matrix by controlled thermal annealing. The heterophase carbon shell effectively alleviates the stress concentration and inhibits crack propagation, which renders our composite superior mechanical properties and high fatigue resistance (106 compression cycles at 20% strain with high stress of 144 kPa, or 5 × 105 cycles at 50% strain with stress up to 260 kPa). This study provides a deep understanding of amorphous-crystalline phase transition and insight into utilizing phase engineering to design and develop other high-performance functional materials such as structural materials and catalysis.