The new green biobased pentamethylene diisocyanate (PDI) trimer curing agent has lower-life-cycle carbon emissions than the petrochemical-based hexamethylene diisocyanate (HDI) trimer curing agent, and its performance is similar to that of petrochemical-based products. This work focused on the synthesis, allophanate modification, free PDI monomer removal, and coating performances of PDI isocyanurate trimers. The results showed that optimal synthesis of PDI isocyanurate trimers used 2-hydroxypropyltrimethylisooctanoate ammonium salt (TMR) as a catalyst with 0.4 wt ‰ added and a reaction time of 120 min. The best free PDI monomer removal by molecular distillation used a removal temperature of 130 °C, a scraper speed of 350 rpm, and a feed rate of 3 mL·min–1, with two total removals. Self-made and allophanate-modified PDI isocyanurate trimers showed high values in physical and chemical properties. The water resistance, acid and alkali resistance, and aging resistance of the self-made and allophanate-modified PDI isocyanurate trimers were similar to or even better than those of petrochemical-based HDI products. These results indicate the application potential of biobased PDI-trimer curing agents.