This research was primary motivated by limited efforts to understand the effects of secondary flow and flow unsteadiness on the heat transfer and the performance of a turbocharger turbine subjected to pulsatile flow. In this study, we aimed to investigate the influence of exhaust manifold on the flow physics and the performance of its downstream components, including the effects on heat transfer, under engine-like pulsatile flow conditions. Based on the predicted results by detached eddy simulation (DES), qualitative and quantitative flow fields analyses in the scroll and the rotor's inlet were performed, in addition to the quantification of turbine performance by using the flow exergy methodology. With the specified geometry configuration and exhaust valve strategy, our study showed that (1) the exhaust manifold influences the flow field and the heat transfer in the scroll significantly and (2) although the exhaust gas blow-down disturbs the relative flow angle at rotor inlet, the consequence on the turbine power is relatively small.