Home-synthesized carbon aerogels were used as reinforcements for epoxy nanocomposites in different weight contents (0.1, 0.3, and 0.5 wt%). The relationship between physical structure of aerogels (specific surface area and total pore volume) and mechanical properties of nanocomposites were evaluated. The fracture toughness of nanocomposites was investigated by both direct and indirect methods. The nanocomposites provided better mechanical properties than neat epoxy. Due to the penetration of polymer chains into the aerogels’ pores, the filler/polymer interface was increased, which lead to an effective increase in load transfer. The porous structure of the aerogels absorbs energy and external force applied, which ultimately plays a role in properties improvement. Due to the higher specific surface area of CNT-doped carbon aerogels (CNT-CA), Ep/CNT-CA nanocomposites showed a better performance. Improvement of fracture toughness in 3-point bending test was greater than impact test. Mechanical and topographical investigations of nanocomposites showed enhancements: 106–143% KIC, 241–372% GIC, 50–58% impact strength and 10.28–14.72 nm roughness, compared to the epoxy matrix.