As a low-cost scheme for small-scale hydropower generation, pump as turbines (PATs) are used at different hydrosites around the world. Nevertheless, a big number of recently conducted studies on PAT performance have mainly focused on the centrifugal type, despite the fact that the axial-flow type has a comparatively large flow capacity, thus disposing of higher power density. Therefore, this article seeks to investigate the flow dynamics of an axial-flow PAT and associated energy loss characteristics, under both pump and turbine operating modes. It adopts the numerical simulation method and uses entropy production theory to propose an energy loss intensity model in the cylindrical coordinate system, which quantitatively gives the spatial variation pattern for energy losses in pump and turbine operating modes. In addition, the correlation between energy loss and flow instability is deeply analyzed, where the energy characteristics in pump and turbine modes are quantitatively evaluated. It is shown that the energy loss within the impeller and the guide vane flow fields, for both operating modes, is mainly because of the turbulent entropy production. The proportion of direct entropy production and wall entropy production is found to be relatively small. The velocity gradient, flow vorticity, turbulence intensity, and energy losses within the flow passages of the axial-flow PAT have been closely related. However, owing to the difference in PAT operating modes, there is a significant difference in the location of energy losses. The unstable flow phenomena, such as the impact at the blade inlet, flow deviation at the blade outlet, flow separation, back-flow, and vortex, are the main reasons for entropy production. This study serves as a reference for the design, optimization, and application of axial-flow PATs.