Epoxy nanocomposites hold immense promise for advanced high-performance applications in coatings, adhesives, and fiber-reinforced composite matrices. However, their widespread use is hindered by low fracture toughness, attributed to highly cross-linked network structure. Here, this study presents a synergistic manufacturing strategy combining ultrasonic graphite-nanocellulose assembly and bidirectional freeze casting to fabricate epoxy nanocomposites with remarkable layered architectures. Subsequent infiltration and curing with epoxy prepolymer produce nanocomposites exhibiting a fracture toughness 4.67 times higher than pure epoxy. Both experimental and theoretical analyses demonstrate the nanocomposite's superior crack propagation resistance, attributable to a range of synergistic toughening mechanisms. These include robust interfacial bonding and mechanical interlocking, which arise from fiber pull-out/flake fracture effects, effectively impeding crack growth. Additionally, the distinctive layered architecture promotes tortuous crack pathways, optimizing fracture energy dissipation. This work offers pivotal insights into structure–property relationships, paving the way for the design of next-generation nanocomposites with tailored, superior mechanical performance.