Highly cross-linked inorganic and organic hybrid cyclomatrix-polyphosphazenes microspheres (C-PPZs) have been successfully synthesized by a one-pot polymerization technique between hexachlorocyclotriphosphazene and p-phenylenediamine in the presence of triethylamine (TEA), and they were used for enhancing the flame retardancy of epoxy resins (EPs). A thermoset EP was prepared by incorporating different percentages (2, 5, and 10%) of C-PPZs into diglycidyl ether of bisphenol A (DGEBA). The results reveal that the size and morphology of the microspheres can be tuned by varying the synthesis temperature. The average size of C-CPPZs gradually increased from 3.1, 4.9, to 7.8 μm as the temperature was increased from 100, 120, to 200 °C, respectively. The thermogravimetric analysis showed that the C-CPPZ microspheres have good thermal stability up to 900 °C with about ∼10 wt % mass loss for C-CPPZs formed at 200 °C compared to ∼30 wt % mass loss for those obtained at 100 and 120 °C. The 10% loss at 900 °C is much lower than the previous research concerning the thermal stability of cyclophosphazene, in which more weight losses were observed at lower temperatures. The resulting C-CPPZ microspheres were characterized by spectroscopic and imaging techniques including Fourier transform infrared spectroscopy, Raman spectroscopy, X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, elemental mapping, and X-ray photoelectron spectroscopy.