In this study, we fabricated a flexible 3D mesh structure with periodic voids by using a 3D lithography method and applying it to a vibration energy harvester to lower resonance frequency and increase output power. The fabrication process is mainly divided into two parts: three-dimensional photolithography for processing a 3D mesh structure, and a bonding process of piezoelectric films and the mesh structure. With the fabricated flexible mesh structure, we achieved the reduction of resonance frequency and improvement of output power, simultaneously. From the results of the vibration tests, the meshed-core-type vibration energy harvester (VEH) exhibited 42.6% higher output voltage than the solid-core-type VEH. In addition, the meshed-core-type VEH yielded 18.7 Hz of resonance frequency, 15.8% lower than the solid-core-type VEH, and 24.6 μW of output power, 68.5% higher than the solid-core-type VEH. The advantage of the proposed method is that a complex and flexible structure with voids in three dimensions can be relatively easily fabricated in a short time by the inclined exposure method. As it is possible to lower the resonance frequency of the VEH by the mesh structure, use in low-frequency applications, such as wearable devices and house appliances, can be expected in the future.