Arranging molecules into highly symmetric, topological crystal structures has been recognized as the best approach to functionalize electronic properties in molecular crystals, where the constituent molecules have been assumed to be rigid in shape. Here, in striking contrast, we demonstrate that the molecules in a monolayer organic crystal can undergo a significant deformation in proximity to the substrate, which is reflected by an asymmetry in the electron density profile. X-ray reflectivity and X-ray absorption spectroscopies in conjunction with density-functional theory calculations reveal that the highly planarized π-core are deformed into a bent shape, while the bulk lattice parameters are maintained. The molecular shape change is found to be perfectly suppressed in a bilayer single crystal, which leads to a 40% increase in mobility in the bilayer crystal. Our finding of a unique, sub-molecular scale shape change in monolayer single crystals can offer possibilities for functionalizing electrical properties via nano-scale physisorption.