The use of thermosetting polymer composites and adhesives in structural applications such as electric cars is limited by the poor toughness of the polymer due to its highly crosslinked structure. The addition of a small weight fraction of silica nano-particles to thermoset polymers is a highly effective means of improving the toughness and mechanical properties of the polymer, but not seen with micro-sized particles. This effect has been investigated using experiments and numerical analysis. The ‘plasticity’ seen in experimental results can be attributed to the debonding of the particles and a debonding criterion is found to be the initiation fracture energy to debond a silica particle. The microstructure has been examined to determine the dispersion of the nano-particles both quantitively and qualitatively, and some differences have been observed. These differences have been investigated using numerical simulations, and different values of strain energy are found in the particles for different small-scale microstructures. The results of these simulations can explain the effect of adding a small weight fraction of nano-sized particles to polymers due to small scale clustering. This new analysis can increase the confidence in the ability to achieve consistently high levels of fracture toughness and mechanical properties for these nano-particle composites.