Polyimide is one of the most important high-performance polymers, which is widely used due to its excellent mechanical performance and thermal stability. Unlike the conventional synthetic approach, hydrothermal polymerization enables the synthesis of polyimides without any toxic solvent and catalyst. Herein, we report the synthesis of polyimide-based microparticles (PIMs) through one-pot hydrothermal polymerization using precursors of mellitic acid (MA) and three isomers of phenylenediamine (PDA) (o-, m-, and p-PDA). Interestingly, the chemical composition of PIMs was highly tunable with the choice of the PDA isomers, leading to considerable morphological differences between PIMs. The molecular dynamics simulation and density functional theory calculation of the polymeric segment of the respective PIMs suggested that the relative ratio of amide to imide influenced the rotational freedom of the polymeric chains and number of hydrogen bonds, resulting in the well-defined structures of respective PIMs. Considering the highly tunable nature of PIMs coupled with the facile synthetic protocol, we anticipate prospective potentials of PIMs in materials, energy, and composite applications.