Abstract Tuning the near-infrared (NIR) emission of organic nanomaterials is of great interest due to possible use in biosensing and imaging based on the biological window ranged in 650–900 nm. In this study, we report NIR fluorescent organic nanoparticles prepared on the basis of ion association between an extended π-conjugated Styryl-9 cation and tetrakis(4-fluorophenyl)borate (TFPB) anion. Binding of Styryl-9 with TFPB results in the prominent appearance of an absorption band that can be assigned to a non-fluorescent H-aggregate, which is revealed by simultaneous deconvolution of both UV–vis absorption and fluorescence excitation spectra, and supported by quantum chemical calculations. Emission is observed in the NIR region from the nanoparticles, but is reduced by the presence of the H-aggregates. To mitigate the H-aggregation occurred inside the nanoparticle, photochemically-inert, bulky tetraphenylphosphonium cation (co-cation) is concurrently incorporated (co-doped), resulting in the disappearance of the relevant H-aggregates and thereby yielding controllable fluorescence peak energy and intensity in the NIR region. We believe that such methodology for synthesizing ion-based organic nanoparticles with tunable emission will open an avenue in the development of new types of NIR fluorescent nanomaterials.