Microporous silica membranes offer significant potential for hydrogen (H2) separation. However, the separation performance of such membranes has been critically limited by membrane pore defects due to traditional evaporation-drying methods. In evaporation-drying methods, surface tension creates cohesion-adhesion imbalances, causing non-uniform solvent removal and capillary force to create defects, thereby supporting non-selective gas permeation. This study proposes a novel supercritical-drying technique that reduces non-selective pathways by facilitating the removal of solvents without surface tension. For this purpose, cobalt-doped silica membranes were fabricated on α-alumina substrates and subjected to either supercritical-drying or the evaporation-drying method. The membranes were evaluated for He and N2 single-gas permeance over a temperature range of 200–500 °C. To understand the effect of drying method on the transport mechanism, experimental permeance and activation energy (Ea) data were combined into a transport modeling framework to establish the most representative pore size distribution (PSD) of silica membranes. The validity of the reconstructed PSD was confirmed by the close correspondence between the modeled and experimental Ea and gas permeance values. Further results showed that the supercritical-dried membrane exhibited a higher proportion of 5–6-member siloxane rings (98.75%) and a lesser contribution of 7- to 9-membered rings than the evaporation-dried membrane, indicating a compact and homogeneous microporous structure. Additionally, structural improvement in the supercritical-dried membrane gave rise to ten times reduced Knudsen flow contributions than the evaporation-dried membrane. This work proves that controlled drying techniques can tune subnanometer pore structure and provide a predictive pathway to design high-performance silica membranes.