Novel hybrid fillers composed of nanodiamond (ND) nanocluster-decorated graphene oxide (GO) were fabricated and incorporated in an epoxy matrix using a facile thermoregulatory liquid-liquid extraction method. The hybrid filler provided significant enhancement of mechanical properties, such as flexural strength, flexural modulus, and fracture toughness. In particular, the epoxy composite containing 0.1 wt% of GN hybrid exhibited a stronger mechanical behavior compared to that containing 0.2 wt% of GO. As the GN loading increased, the thermal stability, the integral procedural decomposition temperature, and the activation energy increased as well. The toughening mechanism was illustrated by a microcrack theory based on the microscopic analysis of the fracture surfaces. The presence of ND nanoclusters not only hindered the aggregation of the GO sheets, but also played a crack pinning role in the polymer-matrix composites, which could significantly enhance its fracture toughness.