Pd/SiO2 organic-inorganic hybrid materials were prepared by adding PdCl2 into methyl-modified silica sol. The Pd/SiO2 hybrid materials were characterized by X-ray diffraction (XRD), fourier transform infrared (FTIR) and X-ray photoelectron spectroscopy (XPS). The effects of calcination temperature and Pd-doping on the phase transition of Pd element and the thermal stability of CH3 group in the Pd/SiO2 organic-inorganic hybrid materials were investigated. The results showed that the reduced metallic Pd0 exhibits good thermal stability under H2 atmosphere in the calcination process. Pd element in noncalcined Pd/SiO2 materials exists in PdCl2 form, calcination at 200 °C in a H2 atmosphere produces some metallic Pd0 and calcinations at 350 °C results in the complete transformation of Pd2+ to metallic Pd0. With the increase of calcination temperature, the Pd0 particle sizes increase and the hydrophobic Si−CH3 bands decrease in intensity. As the calcination temperature is greater than or equal to 350 °C, the loading of metallic Pd0 nearly has no influence on the chemical structure but, with the increase of Pd content, the formed Pd0 particle size increases. To keep the hydrophobicity of Pd/SiO2 membrane materials, the optimal calcination temperature is about 350 °C under H2 atmosphere.