In order to meet the regulation needs of power system, the pump-turbine is prone to operate in the S-shaped region during frequent start-up, leading to unit vibration and grid connection failure. In this paper, the S characteristic experiment was carried out, and the entropy production, unstable flow and vortex structure under turbine, runaway, turbine breaking, reverse pump conditions with optimum guide vane opening are detailed analyzed. The relationship between the energy dissipation and flow field characteristics is clarified. The results show that the runner entropy production is the largest in all components, and the wall entropy production is greater than the fluctuating entropy production under turbine condition. With the decrease in discharge, the fluctuating entropy production and wall entropy production first increase and then decrease, reaching the maximum values in the runaway condition. The circumferential movement trend of water enhances, and forms circumferential flow in the vaneless region. The separation vortex formed on the blade suction surface extends from the blade inlet to the middle of the flow channel, inducing a high entropy production. Under the turbine braking condition, the tangential velocity increases rapidly in the vaneless region. The circumferential flow develops into water ring, blocking the water flows into the runner. Under the reverse pump condition, the water flows in the opposite direction, with negative tangential and streamwise velocities. The absolute flow angle becomes obtuse, and a large-scale reverse vortex is formed. The runner inlet is blocked by the water ring, and the flow channel is almost completely filled with the low-speed region. The proportion of the guide vanes entropy production reaches maximum. Unstable flow leads to the increase in vorticity. Separation vortex, bypassed vortex, and reverse flow vortex leads to an increase in VST, forming a high VST region at corresponding positions. Due to the rotational motion accompanying the development of separated vortex, it leads to the increase in CFT. In addition, the circumferential flow and water ring have higher tangential velocities, which can lead to high CFT regions.