Four phenylethynyl-containing thermosetting polyimide monomers, based on aromatic diamines with various molecular structure and 4-phenylethynylphthalic anhydride, were designed and synthesized to investigate their structure-properties relationships from a molecular dynamics perspective. The trifluoromethyl linkage in the diamine moiety of a polyimide gives the highest flexibility whereas the amide linkage imparts the lowest flexibility to the polymer chain. A more flexible polyimide has a lower melting temperature, lower cohesive energy density, lower mechanical properties, and larger the fraction free volume. Besides, intermolecular hydrogen bonding plays a critical role in the maintenance of physical properties. These simulated values show good agreement with experimental data. This project provided an important opportunity to advance the understanding of structure-property relationships of polyimides.