Naphthene-based aromatic-rich fraction was modified by tetrahydronaphthalene and polyethylene glycol to obtain modified materials which were selected to prepare mesophase pitches by a direct condensation method. The structural composition of modified materials were characterized by simulated distillation (SIMDIS), elemental analysis, Fourier transform infrared spectrometry (FTIR) and 1 H nuclear magnetic resonance ( 1 H NMR) spectroscopy. Influences of the naphthenic structures and alkyl chains in modified materials on the formation and development of mesophase structures were investigated by analyzing variations in optical texture, softening point, carbon residue, molecular and microcrystal structure of mesophase pitch. Results showed that the alkyl structures in modified materials treated by tetrahydronaphthalene and polyethylene glycol were mainly naphthenic structures and alkyl chains, respectively. The existence of alkyl structures in modified materials was beneficial for the formation of mesophase with high quality. Moreover, the naphthenic structures had a better improving effect than alkyl chains. Abundant naphthenic structures or an appropriate amount of alkyl chains in feedstock contributed to the preparation of mesophase pitch with large domain structure, low softening point, high carbon residue and ordered microcrystal structure.