Conventional Savonius rotor experiences negative and high static torque coefficient at several rotor angles. To prevail over this issue Helical Savonius hydrokinetic turbine (HSHKT) twisted with 90° is proposed, which is able to avoid excessive shaking due to hydrodynamic forces on blades. Usually, HSHKT have a low efficiency, Therefore to enhance the performance coefficient of the rotor some augmentation techniques are required to be used. In this study modeling of flow-induced stresses on HSHKT are performed through fluid-structure interaction analysis. The maximum hydraulic load and von-Mises stress on rotor are found as 0.79 Mpa and 145.45 Mpa respectively in case of duct with single deflector augmentation techniques. Computation results show that edge of shaft and joint of end plate and shaft rotor experiences zone of high von-Mises stress which leads to fatigue crack in this area. In consequence to that augmentation techniques creates adverse effect on stability, smooth operation and service life of rotor at the higher free stream velocity, which opposes the fact that the rotor performance is enhanced by employing augmentation techniques in certain conditions. In this study, it is found that the possibility of fatigue crack increases at higher free stream velocity while using augmentation techniques.