Interrelations between main chain and side chain packing are studied in a series of comb-like poly(1,4-phenylene-2,5-n-dialkyloxy terephthalate)s (PPAOTs) with C = 6-12 alkyl carbons per side chain by X-ray diffractometry. Two different polymorphic states, called modification A and modification B, are observed depending on thermal treatment and side chain length. For PPAOTs with short side chains (C ≤ 8), modification A is commonly observed. "As synthesized" (solution crystallized) PPAOTs with longer side chains (C ≥ 10) contain mostly modification B while modification A is growing during melt cooling. A solid-solid transition from modification B to modification A is observed above ≈70 °C for the decyl member (C = 10, PPDOT) while modification A converts under ambient conditions slowly to modification B. This indicates that modification B is thermodynamically stable at low temperature while modification A is stable at higher temperature. Crystallographic analysis shows that both modifications are characterized by an orthorhombic unit cell and a long-range ordered layered structure with alternating main chain and alkyl nanodomains. This is confirmed by 2D diffration data for shear oriented PPDOT fibers. The main difference between both modifications is the packing of the side chains which are in a crystalline state for modification B but disordered for modification A. This is concluded from values for the volume per CH2 unit VCH2 in alkyl nanodomains calculated without further assumptions from the obtained lattice parameters. Interestingly, the crystalline packing of the side chains in modification B leads to a significant increase (≈ 20%) in the application relevant π-π spacings within the main chain domains as compared to those for modification A. It is argued that the structure formation process and thermodynamic equilibrium in comb-like polymers might be strongly influenced by a competition of the individual packing tendencies of main and side chains.