Revealing the evolution of nanoscale third bodies confined between sliding surfaces is essential to understanding the friction and electrical properties for solid contacts. Here, with graphite/graphite contacts in structural superlubricity, a state of no wear and ultralow friction, we in situ reveal the morphological evolution of a third body layer introduced by air through measuring friction and conductance during cyclic hold–slide tests. The directional transport of confined molecules causes apparent elastic deformation of the third body layer, leading to local graphite/graphite direct contact. Together with a proposed quantum tunneling effective thickness (deff) model, a constant volume of third bodies with a sub-nm thickness is observed. Our work provides a feasible approach to investigate the kinetics of substances under nanoscale confinement.