The ultra-small axial flow hydraulic turbine is a portable, palm-sized hydraulic turbine that can be applied to low head applications. By redesigning the original runner of this turbine using a method which uniformized the axial flow velocity, we succeeded in improving the performance of the runner. However, the mechanism of the improved performance of the optimized runner was not sufficiently clear; furthermore, the internal flow of the ultra-small axial hydraulic turbine had hardly been elucidated. This study aims to elucidate the internal flow structure of the ultra-small axial flow hydraulic turbine and to clarify the mechanism behind the improved performance of the optimized runner. To this end, we investigated in detail the internal flow structure of the original and optimized runners using PIV measurements and numerical analysis, focusing on the vortex structures. As a result, it was found that losses due to the tip leakage vortex and vortices near the hub at the blade outlet were smaller for the optimized runner than for the original runner. In particular, it was found that the turbine efficiency was greatly improved because vortices due to the swirling flow downstream of the runner were suppressed, and losses resulting from these vortices were thus reduced.