The growth of the silica (SiO2) bilayer (BL) films on transition metal (TM) surfaces creates a new class of two-dimensional (2D) crystalline, self-contained materials that interact weakly with the TM substrate. The BL-silica/TM heterojunction has shown unique physical and chemical properties that can lead to new chemical reaction mechanisms under the sub-nm confinement and broad potential applications ranging from surface protection, nano transistors, molecular sieves to nuclear waste removal. Novel applications of BL-silica can be further explored as a constituent of van der Waals assembly of 2D materials. Key to these applications is an unmet technical challenge to exfoliate and transfer BL-silica films in a large area from one substrate to another without material damage. In this study, we propose a new exfoliation mechanism based on gas molecule intercalation from density functional theory studies of the BL-silica/TM heterojunction. We found that the intercalation of O atoms and CO molecules at the BL-silica/TM interface weakens the BL-silica—TM hybridization, which results in an exponential decrease of the exfoliation energy against the interface distance as the coverage of interfacial species increases. This new intercalation mechanism opens up the opportunity for non-damaging exfoliation and transfer of large area silica bilayers.