The layer-by-layer (LBL) technique was employed for preparing fluorescent microspheres with a core–shell structure by the alternating adsorption of positively charged poly(p-phenylenevinylene) precursor (pre-PPV) and the polyanions onto polymer substrate spheres, followed by the thermal elimination to convert pre-PPV into fluorescent poly(p-phenylenevinylene) (PPV). Weak polyelectrolytes poly(acrylic acid) (PAA) (usually in a partly ionized form) and strong polyelectrolytes poly(sodium-p-styrenesulfonate) (PSS) were used as the anions to space the PPV layers and reduce the fluorescence self-quenching. Flow cytometry, combined with spectroscopy and microscopy, were used to study the structure and photophysical properties of the resulting microspheres. Optimization of the processing factors was carried out. PAA and PSS as weak and strong polyelectrolytes, respectively, displayed very different influence on the final emission of the spheres. Such difference was attributed to different inherent characteristics of PAA and PSS after detailed investigation in many aspects. In addition, the fluorescent spheres were found to have excellent photostability and thermal stability.