In this study, biocompatible and proton-resistant CdSe quantum dots (QDs) assembled on gelatin nanospheres (GNs) have been synthesized by combining the two-step desolvation method with the layer-by-layer assembly technique. The core-shell fluorescent gelatin nanosphere consists of a gelatin core and a four-layer shell of hydrophilic CdSe QDs assembled through polyelectrolytes (PE). The morphology, microstructures, and photostability of the hybrid spheres were further investigated by scanning electron microscopy (SEM), transmission electron microscopy (TEM), fluorospectrometery, and confocal fluorescent microscopy (CFM), respectively. The average diameter of the hybrid QDs-gelatin nanospheres (QDs-GNs) is estimated at 484 ± 40 nm. Our results indicate that the 20 ± 5 nm of the shell is attributed to the four-layer of CdSe QDs assembled through the PE. QD-GNs show a strong photoluminescence with the maximum emission (λ(em)) at 613 nm at the excitation wavelength of 470 nm. The core-shell QDs-GNs are able to resist quenching in acidic solution (pH < 4). Furthermore, core-shell QDs-GNs show a longer lifetime in a broad range of pH values, from 9 to 1. The calculated average lifetime (τ(ave)) of QDs-GNs is about 889 ± 23 ps, which is 3-fold longer than that of MUA-QDs (263 ± 10 ps) at pH 7.0. The enhanced lifetime of QDs-GNs is almost 9 times of that of CdSe QDs when pH value is 1. Meanwhile, the cell viability study shows that no significant toxic effect is imposed on the NIH/3T3 mouse fibroblast cell line when the concentration of QD-GNs is below 5 mg/mL. It is expected that this new biocompatible fluorescent nanospheres could be an excellent alternative fluorescent imaging agent for cell labeling, especially in acidic conditions.