Applications of conjugated polymer nanoparticles (Pdots) for imaging and sensing depend on their size, fluorescence brightness and intraparticle energy transfer. The molecular design of conjugated polymers (CPs) has been the main focus of the development of Pdots. Here we demonstrate that proper control of the physical interactions between the chains is as critical as the molecular design. The unique design of twisted CPs and fine-tuning of the reprecipitation conditions allow us to fabricate ultrasmall (3.0–4.5 nm) Pdots with excellent photostability. Extensive photophysical and structural characterization reveals the essential role played by the packing of the polymer chains in the particles in the intraparticle spatial alignment of the emitting sites, which regulate the fluorescence brightness and the intraparticle energy migration efficiency. Our findings enhance understanding of the relationship between chain interactions and the photophysical properties of CP nanomaterials, providing a framework for designing and fabricating functional Pdots for imaging applications.