This work aims to investigate the synergistic effects of hybrid bio-fillers and compatibilizers on the properties of natural rubber composites. Rice husk silica (RSi) and hydroxyapatite (HA), derived from rice husk ash and seabass fish scales, respectively, were successfully prepared and used as bio-fillers. Poly(acrylic acid-co-acrylamide)-grafted deproteinized natural rubber (gDPNR) was synthesized via emulsion graft copolymerization, achieving a grafting efficiency and grafting percentage of 15.94 and 4.23%, respectively. The gDPNR was utilized as a compatibilizer in the preparation of natural rubber composites. The addition of hybrid bio-fillers at an RSi-to-HA ratio of 25:75 exhibited superior mechanical properties compared to composites containing a single filler. The incorporation of gDPNR improved filler dispersion and interfacial adhesion between the NR matrix and the bio-fillers, further enhancing the mechanical, thermal, and dielectric properties. The composite with hybrid bio-fillers and 10 phr of gDPNR exhibited the highest tensile strength, showing a 2.10-fold and 1.06-fold improvement over neat natural rubber composite and hybrid filler composite without compatibilizer, respectively. The presence of polar functional groups in gDPNR enhanced the dielectric constant of the natural rubber composites. These composites could have potential in sustainable industrial applications, including flexible electronics and eco-friendly devices.