The piezoelectric nanogenerator (PNG) has been spotlighted as a promising candidate for use as a sustainable power source in wireless system applications. For the further development of PNGs, structural optimization is essential, but the structural analysis progress in this area has been scant. In the present study, we proposed a PNG with a well-ordered nanoshell array structure. The nanoshell structure has been considered as an effective core nanostructure for PNGs due to its effective stress confinement effect but has not been experimentally introduced thus far due to the challenging fabrication method required. To produce a controllable nanoshell structure, a top-down silicon nanofabrication technique which involves advanced spacer lithography is introduced. A comprehensive design strategy to enhance the piezoelectric performance is proposed in terms of the nanoshell diameter and shell-to-shell space. Both simulated and measured data confirm that an extremely high density of a structure is not always the best answer to maximize the performance. The highest amount of power can be achieved when the shell diameter and shell-to-shell space are within their proper ranges. The structural design strategy studied in this work provides a guideline for the further structural developments of PNG.