The microscopic structures of highly crosslinked sulfonated poly(styrene-co-divinylbenzene) resins have been modeled by generating atomistic microstructures using stochastic-like algorithms, which are subsequently relaxed using molecular dynamics. Two different generation algorithms have been tested. The relaxation of the microstructures generated by the first algorithm, which is based on a homogeneous construction of the resin, leads to a significant overestimation of the experimental density as well as to an unsatisfactory description of the porosity. In contrast, the generation approach that combines algorithms for the heterogeneous growing and branching of the chains enables the formation of crosslinks with different topologies. In particular, the intrinsic heterogeneity observed in these resins is efficiently reproduced when the topological loops, which are defined by two or more crosslinks closing a cycle, are present in their microscopic description. Thus, the apparent density, porosity and pore volume estimated using microstructures with these topological loops, called super-crosslinks, are in very good agreement with the experimental results. Although the backbone dihedral angle distribution of the generated and relaxed models is not influenced by the topology, the number and type of crosslinks affect the medium- and long-range atomic disposition of the backbone atoms and the distribution of sulfonic groups. An analysis of the distribution of the local density indicates that super-crosslinks are responsible for the heterogeneous homogenization observed during the MD relaxation. Finally the π-π stacking interactions have been analyzed. Results indicate that those in which the two rings adopt a T-shaped disposition are considerably more abundant as compared to those with the co-facially oriented rings, independently of the resin topology.