Polymer-derived ceramic (PDC) thin films are promising wear-resistant coatings for protecting metals and carbon–carbon composites from corrosion and oxidation. However, the high pyrolysis temperature hinders the applications on substrate materials with low melting points. We report a new synthesis route for PDC coatings using initiated chemical vapor deposited poly(1,3,5-trivinyl-1,3,5-trimethylcyclotrisiloxane) (pV3D3) as the precursor. We investigated the changes in siloxane moieties and the network topology, and proposed a three-stage mechanism for the thermal annealing process. The rise of the connectivity number for the structures obtained at increased annealing temperatures was found with strong correlation to the enhanced mechanical properties and thermal conductivity. Our PDC films obtained via annealing at 850 .C exhibit at least 14.6% higher hardness than prior reports for PDCs synthesized below 1100 .C. Furthermore, thermal conductivity up to 1.02 W (mK).1 was achieved at the annealing temperature as low as 700 .C, which is on the same order of magnitude as PDCs obtained above 1100 .C. Using minimum thermal conductivity models, we found that the thermal transport is dominated by diffusons in the films below the percolation of rigidity, while ultra-short mean-free path phonons contribute to the thermal conductivity of the films above the percolation threshold. The findings of this work provide new insights for the development of wear-resistant and thermally conductive PDC thin films for durable protection coatings.