Summary: The phase behavior of poly(p‐phenylene terephthalate)s (PPT) with pendant side groups, N‐(4‐nitrophenyl)ethylaminoethanol (NPE) and N‐(4‐nitrophenyl)‐L ‐prolinol (NPP) has been studied by using differential scanning calorimetry (DSC), wide‐angle X‐ray scattering (WAXS), and second harmonic generation (SHG). PPT‐NPE showed a layered liquid crystalline morphology while PPT‐NPP showed a completely amorphous structure. Compressive or shear stress applied on the polymer melt surface at 210 °C induced a more prominent layered structure of PPT‐NPE whereas the amorphous structure of PPT‐NPP remained unchanged under the stress. In order to understand this phase difference in terms of the repeat structure, we attempted theoretical ab initio Hartree‐Fock, and DFT calculations for the monomers and molecular dynamics for the bulk state. The results indicated that molecular configurations are a good way of microscopically understanding the phases of rigid backbone polymers with functional side groups: The NPT (constant particle number, pressure, and temperature) simulation data at 210 °C agree qualitatively with the experimental data and the difference between PPT‐NPE and PPT‐NPP could be understood using rotational energy barrier, steric hindrance and inter‐chain interactions. X‐ray diffractometer (XRD) simulation patterns for the oligomers are also in qualitative agreement with the experimental WAXS data and the structural parameters of stacks of PPT‐NPE chains are estimated to be layer distance (4.6 Å), backbone distance (21.5 Å), and side distance (12 Å).