As a liquid residual pressure energy recovery device, hydraulic turbine is widely used in the field of small hydropower construction and energy recovery, but its internal energy loss characteristics are unclear. The two-stage radial hydraulic turbine was taken as the research object. Based on the entropy production theory, the energy loss in each flow component was quantitatively analyzed, and the energy dissipation mechanism in the turbine was further revealed by combining the Omega vortex identification criterion and flow field distribution. The results showed that velocity pulsation and wall effect were the primary sources of energy dissipation. The total proportion of the two was 98.03% under the design condition. The impeller and the guide vane were the main areas of energy dissipation in the turbine; the impeller loss accounted for a higher percentage in the small flow condition, while the guide vane loss accounted for a higher percentage in the large flow condition. The energy loss in the impeller originated from the unstable flow phenomena such as vortex separation at the leading edge of the blade, return vortex at the suction surface, and vortex at the trailing edge of the blade, and the matching of the relative liquid flow angle and the angle of placement of the inlet of the blade was the fundamental reason for the unstable flow in the impeller; in the guide vane Ⅰ and the guide vane Ⅱ-anti-guide vane, the factors leading to the dissipation of their energy at different flow rates were basically the same, and the poor flow such as the stagnation vortex at the leading edge of the blade and the flow separation. The momentum exchange caused by the blade leading edge stall vortex and flow separation was the main cause of energy loss. Due to the asymmetry of the flow inside the annular suction chamber, the entropy yield distribution in each channel of the guide vane Ⅰ was not uniform, while the guide vane Ⅱ-anti-guide vane reduced the shock effect through the rectification of the positive guide vane, and the entropy yield distribution in each channel was uniform and the high entropy area was small.