Reported here is the low-temperature growth of multiple-stack high-density ZnO nanoflower/nanorod structures on polyethylene naphthalate (PEN) substrates derived from the surface modification of ZnO seed layers using an atmospheric-pressure plasma jet (APPJ) treatment. The plasma treatment could provide several advantages to the growth of multiple-stack ZnO nanoflower/nanorod structures: (i) the surface wettability of the seed layers changes from hydrophobic to hydrophilic, resulting in higher surface energies for the growth of high-density ZnO nanoflowers, (ii) the nucleation sites increase due to the increased surface roughness caused by the plasma etching, and (iii) there is no thermal damage to the plastic substrate from the plasma treatment due to its low-temperature weakly ionized discharge. It was also confirmed that multiple stacks of ZnO nanoflowers were obtained without degradation of the crystal quality or modification to the crystal shape or phase. The ZnO nanoflower/nanorod structures grew by lengths up to 4 μm due to an increased surface roughness of 10% and surface energy 5.5 times that of the seed layers. As shown, the APPJ is a very good method to obtain high-density ZnO nanostructures on plastic substrates below 150 °C, as is critical for flexible electronics.