Bis(triethoxysilyl)methane (BTESM), which consists of Si–C–Si bonds, was used as a membrane precursor to control the size of amorphous silica networks. The single gas permeation characteristics of hybrid silica membranes were examined to determine the effect of silica precursors on amorphous networks. Pore size distribution, as determined by single gas permeation, suggested that average pore size was in the following order: bis(triethoxysilyl)ethane (BTESE)-derived silica > BTESM-derived silica > tetraethoxysilane (TEOS)-derived silica, due to differences in the minimum units of the silica precursor. The high C3H6/C3H8 separation performance of BTESM-derived silica membranes in a wide temperature range (50–200 °C) can be due to the control of silica network size by the “spacer” method using a Si–C–Si unit. For example, a BTESM-derived silica membrane showed a high C3H6 permeance of 6.32 × 10–7 mol m–2 s–1 Pa–1 with a C3H6/C3H8 permeance ratio of 8.8 at 50 °C. The order of C3H6 and C3H8 permeances of BTESM-derived silica membranes was C3H6 > C3H8, independent of the number of sol coats and temperature (50–200 °C), although the kinetic diameter of C3H6 (d k = 0.45 nm) was reported to be larger than that of C3H8 (d k = 0.43 nm). For permeation of hydrocarbons through amorphous silica membranes, it is suggested that the kinetic diameter, which is a minimum equilibrium cross-sectional diameter, is not applicable for effective molecular size, probably because diffusivity depends not only on the minimum cross section but also on molecular length.