Abstract: Mesophase pitch-based carbon fibers (MPCFs) have a high modulus of elasticity, low electrical resistivity and high thermal conductivity, so can be used in many fields. Carbon fibers were prepared from two naphthalene-based mesophase pitches, one synthesized by a HF/BF₃ catalytic one-step method (AR-MP) and the other by an AlCl₃ catalytic two-step method (N-MP). The mesophase pitches, spun pitch fibers, pre-oxidized fibers, carbonized fibers and graphitized fibers produced from them were characterized by TG-MS, FT-IR, ¹³C-NMR, MALDI-TOF-MS, XRD, SEM and elemental analysis. The molecular structures and properties of mesophase pitches were compared, and the effects of molecular structures on the structures and properties of the carbon fibers produced from them were measured. In comparison to N-MP, AR-MP has a rod-like semi-rigid molecular configuration containing more naphthenic structures and methyl side chains. The pre-oxidized fibers derived from AR-MP have a better carbon layer orientation, so that their graphitized fibers have a higher thermal conductivity of 716 W/(m·K). N-MP has a higher aromaticity with a disc-like rigid molecular configuration, so that the graphitized fibers prepared from it have a higher tensile strength of 3.47 GPa due to fewer defects being formed during preparation. The molecular structures of AR-MP and N-MP have an obvious influence on the structures and properties of their graphitized fibers.