Molecular dynamics simulations and experimental measurements were used to investigate the thermal and mechanical properties of cross-linked phenolic resins as a function of the degree of cross-linking, the chain motif (ortho–ortho versus ortho–para), and the chain length. The chain motif influenced the type (interchain or intrachain) as well as the amount of hydrogen bonding. Ortho–ortho chains favored internal hydrogen bonding whereas ortho–para favored hydrogen bonding between chains. Un-cross-linked ortho–para systems formed percolating 3D networks of hydrogen bonds, behaving effectively as “hydrogen gels”. This resulted in differing thermal and mechanical properties for these systems. As cross-linking increased, the chain motif, chain length, and hydrogen bonding networks became less important. Elastic moduli, thermal conductivity, and glass transition temperatures were characterized as a function of cross-linking and temperature. Both our own experimental data and literature values were used to validate our simulation results.