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Despite their importance, chemical reactions confined in a low dimensional space are elusive and experimentally intractable. In this work, we report doubly anisotropic, in-plane and out-of-plane, oxidation reactions of two-dimensional crystals, by resolving interface-confined thermal oxidation of a single and multilayer MoS2 supported on silica substrates from their conventional surface reaction. Using optical second-harmonic generation spectroscopy of artificially stacked multilayers, we directly proved that crystallographically oriented triangular oxides (TOs) were formed in the bottommost layer while triangular etch pits (TEs) were generated in the topmost layer and that both structures were terminated with zigzag edges. The formation of the Mo oxide layer at the interface demonstrates that O2 diffuses efficiently through the van der Waals (vdW) gap but not MoO3, which would otherwise sublime. The fact that TOs are several times larger than TEs indicates that oxidation is greatly enhanced when MoS2 is in direct contact with silica substrates, which suggests a catalytic effect. This study indicates that the vdW-bonded interfaces are essentially open to mass transport and can serve as a model system for investigating chemistry in low dimensional spaces.