Two-dimensional (2D) atomic crystal superlattices integrate diverse 2D layered materials enabling adjustable electronic and optical properties. However, tunability of the interlayer gap and interactions remain challenging. Here we report a solution based on soft oxygen plasma intercalation. 2D atomic crystal molecular superlattices (ACMSs) are produced by intercalating O2+ ions into the interlayer space using the plasma electric field. Stable molecular oxygen layer is formed by van der Waals interactions with adjacent transition metal dichalcogenide (TMD) monolayers. The resulting interlayer gap expansion can effectively isolate TMD monolayers and impart exotic properties to homo-(MoS2[O2]x) and hetero-(MoS2[O2]x/WS2[O2]x) stacked ACMSs beyond typical capacities of monolayer TMDs, such as 100 times stronger photoluminescence and 100 times higher photocurrent. Our potentially universal approach to tune interlayer stacking and interactions in 2D ACMSs may lead to exotic superlattice properties intrinsic to monolayer materials such as direct bandgap pursued for future optoelectronics.