Since the performance of the micro-thermophotovoltaic (TPV) system is significantly limited by the mismatch between the radiation spectrum and the photovoltaic (PV) bandgap, for the first time, a wideband and angle-insensitive metamaterial filter was developed and optimized to address this issue. The developed filter was placed between the reactor and the PV cell and it was able to effectively transmit the valuable photons for power generation and reflect the worthless energy, thus offering great potential to improve the performance of the micro-TPV system. In particular, the filter is applicable for the entire near infrared wavelength range and exhibits extraordinary transmission. For the working wavelength applied in this paper, the obtained peak transmission coefficient from experiments is up to 88.3%. Furthermore, the efficiency of the micro-TPV system is also predicted to be enhanced more than twice with the metamaterial filter applied. Both the experimental and theoretical results show that the incorporation of the metamaterial filter with low bandgap PV cells can be a promising approach to improve the efficiency of the existing micro-TPV system.