The cooperative Jahn-Teller effect (CJTE) refers to the correlation of distortions arising from individual Jahn-Teller centres in complex compounds(1,2). The effect usually induces strong coupling between the static or dynamic charge, orbital and magnetic ordering, which has been related to many important phenomena such as colossal magnetoresistance(1,3) and superconductivity(1,4). Here we report a Na5/8MnO2 superstructure with a pronounced static CJTE that is coupled to an unusual Na vacancy ordering. We visualize this coupled distortion and Na ordering down to the atomic scale. The Mn planes are periodically distorted by a charge modulation on the Mn stripes, which in turn drives an unusually large displacement of some Na ions through long-ranged Na-O-Mn3+-O-Na interactions into a highly distorted octahedral site. At lower temperatures, magnetic order appears, in which Mn atomic stripes with different magnetic couplings are interwoven with each other. Our work demonstrates the strong interaction between alkali ordering, displacement, and electronic and magnetic structure, and underlines the important role that structural details play in determining electronic behaviour.