Since the small hydro power is expected promising, the authors devised ultra-small axial flow hydraulic turbine that can be applied to low head and small flow rate. In this research, we aim to clarify the detailed internal flow structure by advanced measurement and numerical analysis to improve turbine efficiency. Therefore, we measured flow velocity by particle image velocimetry (PIV) for Original and Optimized runners in the actual machine experiment. At the same time, we performed numerical analysis and confirmed the validity of the experimental and numerical analysis based on the obtained results. On that basis, we focused on the vortex structure from the results of numerical analysis, and visualized internal flow structure, and investigated loss mechanism by comparing both runners, so we obtained the following findings. Experimental and calculated values of axial flow velocity distribution agree well for time average and instantaneous at runner inlet and outlet. From the authors’ numerical analysis, Optimized runner has smaller loss due to the tip leakage vortex than Original one. Particularly, Optimized runner suppresses the vortex caused by the swirling flow at the downstream of the runner, and the loss caused by it decreased, so the turbine efficiency improved greatly.