The mechanical properties and internal structure of soot nanoparticles is investigated using reactive molecular dynamics simulations of nanoindentation of model soot particles. The particles that are provided as inputs to the simulations are generated using reactive molecular dynamics to create 3D networks of crosslinked coronene, circumanthracene and core-shell mixtures of coronene and circumanthracene. The results of the simulated nanoindentation experiments are analysed as a function of the degree of crosslinking (defined as the number of crosslinks per monomer in the particles), the size and the core-shell structure of the particles. In the case of homogeneous particles (i.e. those without a core-shell structure), the simulations show a unique relationship between the degree of crosslinking (CL) and the simulated hardness, Young’s modulus and deformation ratio. In the case of particles with a core-shell structure, a unique relationship was only found by considering the core-shell ratio and the degree of crosslinking in both the core and the shell. Our results allow for interpretation of the nanoindentation experiments as suggesting crosslinks are present in mature soot particles and preliminary evidence that crosslinks also are present within the interior of soot particles.