Nanoparticles derived from π-conjugated polymers have gained widespread attention as active layer materials in various organic electronics applications. The optoelectronic, charge transfer, and charge transport properties of π-conjugated polymers are intimately connected to the polymer aggregate structure. Herein we show that the internal aggregate structure of regioregular poly(3-hexylthiophene) (P3HT) within polymer nanoparticles can be tuned by solvent composition during nanoparticle fabrication through the miniemulsion process. Using absorption spectra and single-NP photoluminescence decay properties, we show that a solvent mixture consisting of a low boiling good solvent and a high boiling marginal solvent results in polymer aggregate structure with a higher degree of uniformity and structural order. We find that the impact of solvent on the nature of P3HT aggregation within nanoparticles is different from what has been reported in thin films.