We constructed and characterized a network structure of crosslinked phenolic resins using a large-scale atomistic molecular dynamics simulation with a pseudo-reaction algorithm. The atomic configuration of the reaction products was controlled by the reaction probabilities and initial molecular structures. The crosslinked structure obtained from phenols as initial molecules agreed well with experimental results in terms of the branching structure of the phenolic units and the methylene linkages, molecular weight distributions, densities, and scattering functions at various reaction conversions. The calculated structure factor for phenolic resins indicated inhomogeneous crosslinking, which expanded as the reaction proceeded after gelation. Voronoi tessellation analysis of the change in the occupation volume of the phenolic units after crosslinking indicated that the initial molecular configuration influenced the resulting crosslinked structure. The experimental molecular weight distribution before gelation and the scattering function were well reproduced by a large-scale simulation with 232,000 atoms. (C) 2016 Elsevier Ltd. All rights reserved.