Polyimides (PIs) are in high demand in the field of active matrix organic light-emitting diode displays because of their excellent heat resistance, chemical stability, and mechanical properties. However, the most critical key to their application is to further enhance their glass transition temperature (Tg), which directly affects the processing temperature of thin-film transistors on the PI films. Therefore, it is of great importance to study the factors that have an influence on the Tg of PIs. To accomplish this goal, PIs derived from pyromellitic acid dianhydride and three sets of isomeric imidazole-based diamines were investigated. The investigation, by computational methods, was to clarify the effect of intrinsic factors associated with the molecular structure of the PIs on their Tg and to construct a structure-Tg relationship for these PIs. For each model system, all-atom molecular dynamics simulations were used to identify and distinguish the effects of chain rigidity, fractional free volume (FFV), cohesive energy density, hydrogen-bonding interactions, and charge-transfer complex interactions on Tg. The results showed that the physical property, chain rigidity, has a direct impact on Tg regardless of the polymer backbone structure. A linear correlation between the increase of FFV and the decrease of Tg was not established due to the existence of hydrogen-bonding interactions, but the tendency was maintained. Furthermore, the formation of hydrogen bonds was found to have an indirect relationship with Tg. That is, the increase of intrachain hydrogen bonds would lead to a decrease in chain rigidity and consequently reduce the Tg value.