A miniature thermoelectric energy harvester and a fabrication method thereof. Annular grooves are fabricated on a low-resistivity silicon substrate to define silicon thermoelectric columns, an insulating layer is fabricated on the annular grooves, a thermoelectric material is filled in the annular grooves to form annular thermoelectric columns, and then metal wirings, passivation layers and supporting substrates are fabricated, thereby completing the fabrication process. The silicon thermoelectric column using a silicon base material simplifies the fabrication process. The fabrication of the thermocouple structure is one thin-film deposition process, which simplifies the process. The use of silicon as a component of the thermocouple has a high Seebeck coefficient. The use of vertical thermocouples improves the stability. Since the thermocouple structure is bonded to the upper supporting substrate and lower supporting substrate by wafer-level bonding, the fabrication efficiency is improved.