Pump as turbine (PAT) is a common method of energy recovery, however, vortices are a negative phenom for these units. The objective of this research is to study the effect of vortex motion on the hydraulic loss of pump as turbine, and establishing the correlation mechanism between vortex intensity and turbulence loss. The research method adopts theoretical analysis and model test and numerical simulation. Based on the entropy production theory, the hydraulic loss and the turbulent dissipation in boundary layer induced by vortex motion are studied, revealing the influence of vortices on the energy loss. Results show that the vortex motion can be decomposed into a synchronous component v_sy and a rotational component v_ro, among them, the rotational component v_ro meets to Biot-Savart Law. The turbulent dissipation rate in the boundary layer is closely to the vortex motion, which can characterize the boundary turbulence height. Turbulent flow induced by vortex can propagate in the flow channel of the unit, causing lot of additional hydraulic loss. In the end, a mathematical model between entropy production (Sk) induced by vortex and vortex strength (¿k) was established, indicating that Sk changes with ¿k in the form of a quadratic function.