In a nano filter structure for breathing and a manufacturing method of the nano filter structure, a semiconductor process technology is used for manufacturing a nano filter structure comprising a top gate, a bottom gate, a plurality of sidewall gates and a plurality of supports. The sidewall gates include a plurality of filterable gratings, and the filterable gratings are controlled precisely to a nanoscale by a semiconductor process technology. Therefore, the nano filterable gratings can be manufactured easily and quickly, and the multilayer design of the filterable gratings enhances the aperture ratio of a filter material, such that users can inhale or exhale easily through the filter material.