Flavonoids (FLAs) possess anti-cancer, anti-viral, anti-bacterial, and anti-oxidant properties. In this study, gelatin nanoparticles (GNPs) with controllable surface potential and diameter was prepared through a modified two-step desolvation. Two well-known flavonoids, namely, low-molecular weight Genistein (GEN) and high-molecular weight Icariin (ICA), were adsorbed onto the surface of GNPs (FLA@GNPs). The characteristics of GNPs and the main parameters affecting flavonoid adsorption were studied to evaluate the adsorption capacity and structural stability of FLA@GNPs. Furthermore, co-adsorption of GEN and ICA was detected. The adsorption mechanism of GNPs with FLA was further discussed. Results showed that the low-molecular weight GEN could be effectively adsorbed by GNPs, and their entrapment efficiencies were over 90% under optimized conditions. The total drug loading of the co-adsorbed FLA@GNPs was significantly higher than that of the single drug loaded (GEN or ICA). GEN@GNPs could maintain its structural stability under acidic conditions (pH = 2) at room temperature (25 °C). This protective function enables both ICA and GEN to be bioactive at room temperature for at least 180 days. The characteristics of GNPs adsorption indicate that the hydrogen bonding theory of the combination of gelatin molecules with polyphenols cannot sufficiently explain the binding of GNPs with polyphenols. FLA@GNPs is a promising general-purpose gelatin-based co-loading preload structure with simplified operation and storage condition.