We report a facile and reproducible method to synthesize advanced, homogenized, hybrid, nanoflower of thorium oxide and thorium oxalate hydrate material via a novel, green, microwave irradiated chemical process. The Nanoflowers can be successfully synthesized using thorium nitrate penta hydrate as the metal source along with two different capping agents, cetyltrimethyl ammonium bromide and 4-amino-1H-pyrimidine-2-one respectively in the ubiquity of microwave irradiation having power source 230V at the temperature of 45°C for 15 minutes to get the desired product. The synthesized material was characterized by various complementary techniques namely XRD, FTIR, PL, TGA/DSC curve, SEM and EDX. The 3D nanoflowers structure, so formed, resembles a natural Peony flower. The applications of synthesized material lies in the area of making thorium metal, densified thorium oxide, carbide and nitride, anhydrous thorium complexes and thorium boron silicates glasses.