Low-frequency vibration is widespread in nature. Vibration energy harvesting is considered to be a reliable and sustainable method to achieve continuous power supply. It is a feasible method to design an energy harvesting system of the bio-inspired mechanical structure to improve the efficiency of energy harvesting. A hybrid energy harvester piezoelectric–electromagnetic that mimics the flapping wing motion of the Diptera insect. The biomimetic energy harvesting device consists of two piezoelectric cantilever beams structure with the mass block installed, which mimics the flapping movement mechanism of the Diptera insect. The intermediate part of this harvester inspired by the insect skeleton and muscle structure of the Diptera insect is composed of magnetic levitation coupled repulsion structure, which is easily affected by vibration and changes greatly, to realize electromagnetic energy harvesting. The ‘click’ mechanism of the Diptera insect is constructed by storing energy in springs to improve the performance of energy harvesting devices. The hybrid energy harvesting device realizes piezoelectric–electromagnetic energy harvesting with multiple energy outputs at one excitation input. A dynamic model of the proposed energy harvester is constructed based on the electromechanical coupling characteristics. The modal analysis and structure optimization of this device is realized by the finite element method (FEM). The FEM simulation and experimental results can verify that under the low-frequency excitation of 3 Hz, the maximum output power of the designed harvester reaches 12.33 mW in the low-frequency environment.