Vortices generated during underwater undulatory swimming (UUS) produced thrust and propelled swimmers. Therefore, clarifying how the vortices generated during UUS changed with different swimming velocities was crucial for improving swimming performance. This study aimed to clarify the changes in vortex structure in UUS when test flow velocities (U) were varied. A male collegiate swimmer participated in the trials, and trial swims were performed at three different U (0.8, 1.0, and 1.2 m/s). Particle image velocimetry (PIV) was used to analyze the flow fields behind the swimmer. The flow field was converted into a quasi-three-dimensional flow by performing multiple trials at the same U and averaging the results. The peak value of the vorticity component in the flow field increased with U. The structure of the vortices observed from the end of a down-kick to the beginning of an up-kick changed as U increased, and the direction of the jet flow between the vortex pairs became vertically downward. This phenomenon resembled the C-start maneuver seen in fish, where sudden acceleration prompted a more vertical downward flow direction. Such a change in vortex structure was considered to be a strategy to generate large momentum during an up-kick. This was the first study to quantify the vortex structure during UUS and reveal the variations in vortex structure with changes in swimming velocities, highlighting the importance of the down-kick to up-kick switching phase in UUS from the vortex structure in the flow field perspective.