The developments of two-stage turbocharging and turbocompounding promote the application of the two-stage turbine system in internal combustion engines. Since the turbine suffers from the pulsating exhaust, the performance deteriorates significantly from steady conditions. In the paper, the pulsating flow losses in the two-stage turbine are analyzed and a control method is proposed to improve the turbine performance. ANSYS CFX, which is a commercial software for computational fluid dynamic, is applied to resolve the three-dimensional unsteady flow problem. The accuracy of the simulation method is verified by the experimental data from each turbine. Firstly, the impacts of pulse amplitudes on transient loss of each component of the two-stage turbine are studied. Then flow field analysis is carried out to understand details of the unsteady flows. It is found that the variation of incidence angle at the low-pressure turbine (LPT) rotor tip is significantly larger than that at rotor hub, which causes severe flow loss near leading edge. As a result, the LPT performance drops down significantly. To improve the LPT performance, the blade shape at tip is modified. The aerodynamic performances of turbines with three different shapes under high- and low-load pulsating flow conditions are evaluated. It is found that increased inlet blade angle and medium thickness achieves good aerodynamic performance. The rotor averaged efficiency is improved by 2.27% under high-load pulsating condition.