Semiconducting polymer dots (Pdots) represent a new class of fluorescent nanoparticles for biological applications. In this study, we investigated their size-dependent fluorescence and cellular labeling properties. We demonstrate that the polymer conformation in solution phase largely affects the polymer folding and packing during the nanoparticle preparation process, resulting in solution-phase control over the fluorescence properties of semiconducting polymer nanoparticles. The resulting Pdots exhibit apparent size dependent absorption and emission, a characteristic feature of different chain packing behaviors due to the preparation conditions. Single-particle fluorescence imaging was employed to perform a side-by-side comparison on the Pdot brightness, indicating a quadratic dependence of single-particle brightness on particle size. Upon introducing a positively charged dye Nile blue, all the three type of Pdots were quenched very efficiently (Ksv > 1 × 107 M−1) in an applied quenching process at low dye concentrations, but exhibit apparent difference in quenching efficiency with increasing dye concentration. Furthermore, Pdots of different sizes were used for cell uptake and cellular labeling involving biotin−streptavidin interactions. Fluorescence imaging together with flow cytometry studies clearly showed size dependent labelling brightness. Small-sized Pdots appear to be more effective for immunolabeling of cell surface, whereas medium-sized Pdots exhibit the highest uptake efficiency. This study provides a concrete guidance for selecting appropriate particle size for biological imaging and sensing applications.