Polystyrene-based nanoparticles (PSt NPs) prepared by emulsion polymerization are promising organic matrices for encapsulating over-thousand-nanometer near-infrared (OTN-NIR) fluorescent dyes, such as thiopyrilium IR-1061, for OTN-NIR dynamic live imaging. Herein, we propose an effective approach to obtain highly emissive OTN-NIR fluorescent PSt NPs (OTN-PSt NPs) in which the polarity of the PSt NPs was adjusted by changing the monomer ratio (styrene to acrylic acid) in the PSt NPs and the dimethyl sulfoxide concentration in the IR-1061 loading process. Moreover, OTN-PSt NPs covalently modified with poly(ethylene glycol) (PEG) (OTN-PSt-PEG NPs) showed high dispersion stability under physiological conditions and minimal cytotoxicity. Notably, the optimized OTN-PSt-PEG NPs were effective in the dynamic live imaging of mice. This methodology is expected to facilitate the design of certain polar thiopyrilium dye-loaded OTN-NIR fluorescent imaging probes with high emissivity.