The relationship between charge transport and surface morphology is investigated by utilizing rubrene single crystals of varying thicknesses. In the case of pristine crystals, the surface conductivities decrease exponentially as the crystal thickness increases until ∼4 μm, beyond which the surface conductivity saturates. Investigation of the surface morphology using optical and atomic force microscopy reveals that thicker crystals have a higher number of molecular steps, increasing the overall surface roughness compared with thin crystals. The density of molecular steps as a surface trap is further quantified with the subthreshold slope of rubrene air-gap transistors. This thickness-dependent surface conductivity is rationalized by a shift from in-plane to out-of-plane transport governed by surface roughness. The surface transport is disrupted by roughening of the crystal surface and becomes limited by the slower vertical crystallographic axis on molecular step edges. Separately, we investigate surface-doping of rubrene crystals by using fluoroalkyltrichrolosilane and observe a different mechanism for charge transport which is independent of surface roughness. This work demonstrates that the correlation between crystal thickness, surface morphology, and charge transport must be taken into account when measuring organic single crystals. Considering the fact that these molecular steps are universally observed on organic/inorganic and single/polycrystals, we believe that our findings can be widely applied to improve charge transport understanding.