Detail pore size control for silica composite separation membrane was performed. Silica composite membranes were deposited on porous ceramic substrates by chemical vapor deposition. An organic group is introduced into the silica structure by introducing an organic group into the silica precursor used during membrane preparation. A membrane with a pore diameter of 0.37 nm without organic groups was obtained, which selectively permeated hydrogen. The pore diameters increased to 0.40 nm when propyl groups were introduced as an organic group. Furthermore, the hydrogen permeance also increased to 3.7 times. This vapor deposition phenomenon was investigated by investigating the thermal decomposition behavior of organic groups on hydrated silica powder. The decomposition/deposition behavior changes at low, medium, and high temperatures. Decomposition of organic groups by ozone was observed at a low temperature of about 200 °C. On the other hand, at medium temperatures of about 250 °C, the decomposition of the reaction aid, ozone, progressed, and the decomposition of the organic groups is limited. At high temperatures above 400 °C, thermal decomposition of the organic groups is dominant, and the amount of organic groups in the separation layer is decreasing.