Using the piezoelectric (PZT) effect, energy-harvesting has become possible for phononic crystal (PnC). Low-frequency vibration energy harvesting is more of a challenge, which can be solved by local resonance phononic crystals (LRPnCs). A novel three-dimensional (3D) energy harvesting LRPnC is proposed and further analyzed using the finite element method (FEM) software COMSOL. The 3D LRPnC with spiral unit-cell structures is constructed with a low initial frequency and wide band gaps (BGs). According to the large vibration deformation of the elastic beam near the scatterer, a PZT sheet is mounted in the surface of that beam, to harvest the energy of elastic waves using the PZT effect. To further improve the energy-harvesting performance, a 5 × 5 super-cell is numerically constructed. Numerical simulations show that the present 3D super-cell PnC structure can make full use of the advantages of the large vibration deformation and the PZT effect, i.e., the BGs with a frequency range from 28.47 Hz to 194.21 Hz with a bandwidth of 142.7 Hz, and the maximum voltage output is about 29.3 V under effective sound pressure with a peak power of 11.5 µW. The present super-cell phononic crystal structure provides better support for low-frequency vibration energy harvesting, when designing PnCs, than that of the traditional Prague type.