Coarse-grained molecular dynamics simulations are used to elucidate molecular mechanisms responsible for different mechanical behaviours of elastomers containing spherical particles with different volume fractions. We observe that different filler volume fractions result in qualitatively different responses of the polymer nanocomposite to tensile strain. At relatively low filler volume fraction a yield drop appears in the stress–strain curve. As the filler volume fraction increases there is a reduction in the rate of plastic hardening, becoming plastic softening at sufficiently high filler volume fraction. We demonstrate that these behaviours are a result of the network formed by the polymer chains and filler particles. We identify three distinct molecular structural motifs between polymer and filler particles whose relative prevalence varies with the filler volume fraction and as the system is dynamically strained. We show how this evolution in molecular structure is directly linked to the observed mechanical response.