Microfluidic synthesis methods are among the most promising approaches for controlling the size and morphology of polymeric nanoparticles (NPs). In this work, for the first time, atomistic mechanisms involved in morphological changes of polybenzimidazole (PBI) NPs in microfluidic media are investigated. The multiscale molecular dynamic (MD) simulations are validated with the literature modeling and experimental data. A good agreement is obtained between the molecular modeling results and experimental data. The effects of mixing time, solvent type, dopant, and simulation box size at the molecular level are investigated. Mixing time has a positive impact on the morphology of the PBI NPs. Microfluidic technology can control the mixing time well and engineer the morphology of the NPs. In the process of morphological changes, at the optimum time (about 11.5 ms), the attraction energy between the polymer molecules is at the highest level (-37.65 kJ/mol). The size of the polymer NPs is minimal (2.3 nm), and the aspect ratio and entropy are at the lowest level, equal to 1.07 and 11.024 kJ/mol·K, respectively. It was found that the presence of water leads to the precipitation of polymeric NPs owing to the dominance of hydrophobic forces. Both dimethylacetamide (DMA) and phosphoric acid (PA) improve the control of the size and morphology of NPs. However, the addition of PA has a greater impact; PA acts as a cross-linker, making PBI NPs finer and more spherical. In addition, MD simulation reveals that PA increases the proton diffusion coefficient in PBI and enhances its efficiency in fuel cells. This study paves a new efficient way for morphological engineering of polymeric NPs using microfluidic technology.