We demonstrate the enhancement of output power from a ZnO nanorod (NR)-based piezoelectric nanogenerator by using Si microhole (Si-μH) arrays. The depth-controlled Si-μH arrays were fabricated by using the deep reactive ion etching method. The ZnO NRs were grown along the Si-μH surface, in holes deeper than 20 μm. The polymer layer, polydimethylsiloxane, which acts a stress diffuser and electrical insulator, was successfully penetrated into the deep Si-μH arrays. Optical investigations show that the crystalline quality of the ZnO NRs on the Si-μH arrays was not degraded, even though they were grown on the deeper Si-μH arrays. As the depth of the Si-μH arrays increase from 0 to 20 μm, the output voltage was enhanced by around 8.1 times while the current did not increase. Finally, an output power enhancement of ten times was obtained. This enhancement of the output power was consistent with the increase in the surface area, and was mainly attributed to the accumulation of the potentials generated by the series-connected ZnO NR-based nanogenerators, whose number increases as the depth of the Si-μH increases.