Methyl-modified, cobalt-doped silica (Co/MSiO2) materials were synthesized by sol-gel technique calcined in N2 atmospheres, and membranes were made thereof by coating method. The effects of Co/Si molar ratio (nCo) on the physical-chemical constructions of Co/MSiO2 materials and microstructures of Co/MSiO2 membranes were systematically investigated. The gas permeance performance and hydrothermal stability of Co/MSiO2 membranes were also tested. The results show that the cobalt element in Co/MSiO2 material calcined at 400 °C exists not only as Si–O–Co bond but also as Co3O4 and CoO crystals. The introduction of metallic cobalt and methyl can enlarge the total pore volume and average pore size of the SiO2 membrane. The activation energy (Ea) values of H2, CO2, and N2 for Co/MSiO2 membranes are less than those for MSiO2 membranes. When operating at a pressure difference of 0.2 MPa and 200 °C compared with MSiO2 membrane, the permeances of H2, CO2, and N2 for Co/MSiO2 membrane with nCo = 0.08 increased by 1.17, 0.70, and 0.83 times, respectively, and the perm-selectivities of H2/CO2 and H2/N2 increased by 27.66% and 18.53%, respectively. After being steamed and thermally regenerated, the change of H2 permeance and H2 perm-selectivities for Co/MSiO2 membrane is much smaller than those for MSiO2 membrane.