In this work, we performed molecular dynamics (MD) simulations of nanoindentation on combustion-generated nanoparticles – also known as soot – aimed to investigate the effects of the particle structure on its mechanical properties. More than fifty model nanoparticles with different radius (Rparticle), degrees of crosslinking (CL) and shell thickness (dshell) were built. The hardness of each particle was calculated and the results were compared with nanoindentation experiments of soot particles. The results show that mature soot particles are expected to present crosslinks between their aromatic constituents to have a comparable value of the hardness found experimentally. These results provide valuable information on soot morphology and formation mechanism, revealing the importance of crosslinking reactions during soot maturation that give rise to a structure in which the majority of aromatics are aliphatically-linked.