In order to optimize the molecular structure and composition distribution of mesophase pitch, the two-stage thermotreatment process preparation using boron trifluoride ethyl valerate complex as catalyst was investigated. During the two-stage thermotreatment, the cationic polymerization initiated by catalytic polycondensation made carbonaceous microcrystalline molecules contain more semi-rigid structures, while parts of alkyl side chains and naphthenic structures were retained. Subsequently, the mesophase pitch was rapidly induced to form by removing non-mesogens and enriching sufficient concentrations of mesogens in the vacuum polycondensation stage. The results showed that the two-stage thermotreatment process could change the chemical structure of the aromatic nucleus and obtain a suitable softening point (283 °C) at 100% anisotropic content. The mesophase pitch with 5 wt% catalyst addition (MP-5) had high content of methylene structure (HF = 3.18 wt%), naphthenic structure (HN = 3.45 wt%) and fusible/soluble TI-PS sub-fraction (28.07 wt%). In addition, MP-5 also possessed high aromaticity (fa = 0.90) and stacking order (Lc = 37.48 Å, n = 11.70). Unfortunately, an increase in the oxygen-containing groups was accompanied when the catalyst content reached to 10 wt%, which disrupted the aromatic lamellae parallel stacking structure of the mesophase pitch due to steric hindrance, resulting in more isotropic structures in the product.