In our previous study, we verified that a two-step process was superior to the one-pot process for the manufacture of THTCPD, assuming the pilot-scale production aspect of a comparative economic analysis by using an engineering estimation method to predict the unit manufacturing cost. Among the processes of the two-step process, our study was intended to focus on the isomerization to produce the final THTCPD products with outstanding physical properties including a specific gravity, a heat of combustion, a viscosity and a freezing point. Although HY(30) was used as an isomerization catalyst in the previous study, the catalytic activity of HY(30) did not surpass that of AlCl3 in terms of isomerization conversion, possibly due to lower exo-THTCPD selectivity by Bronsted acid sites of HY(30) than that by Lewis acid sites of AlCl3. However, AlCl3 has some drawbacks of the impossibility for the catalyst regeneration during the manufacturing process due to the difficulty of the catalyst separation and recovery after isomerization, which causes environmental problems and biological toxicity issues due to its corrosivity. Therefore, our study concentrated on catalyst regeneration assuming the real production process in a pilot scale using AlCl3 in comparison with HY(30). Then, we investigated whether the isomerization catalyst AlCl3 or HY(30) was more commercially favorable through a comparative unit production cost prediction applying an engineering estimation in this study. In conclusion, the unit production cost for AlCl3 was lower than that for HY(30) with the fresh catalyst. Reversely, unit production costs for HY(30) with increase in catalysts regeneration number (N) were lower than those for AlCl3 due to the drastic decrease in the unit material cost of HY(30) unlikely with that of AlCl3 due to its non-reusability.