Optimizing the colloidal state of polyamic acid (PAA) nanoparticles is essential for achieving a uniform and high-performance polyimide coating by electrophoretic deposition (EPD) on metal substrates of various shapes. In this paper, we report two important roles of the counterions in the formation of PAA colloids for EPD, which, to date, have not been recognized. First, when tertiary alkyl amines are used to neutralize PAA, the polarity of neutralizing counterions determines the size and stability of the PAA colloidal particles. The polarity can be finely tuned by using two different tertiary alkyl amines containing polar and nonpolar groups and adjusting the molar ratio. Depending on the polar/nonpolar ratio, various states of PAA colloids were obtained, including dissolved state, stable colloid, and aggregates. Second, we observed that the confined counterions inside PAA nanoparticles can act as an imidization catalyst during the thermal annealing process. It is revealed that some fraction of the counterion species, mostly having nonpolar groups, is not drawn toward the counter electrode and remains inside the PAA nanoparticles during the EPD process. Optimizing the polarity eventually allowed us to form uniform EPD coatings with high dielectric strengths.