Variable nozzle turbine (VNT) adjusts the openings of its nozzles to insure the required flow at throat area, which broadens the operating range of the turbine, and improves the matching relationship between the turbocharger and the engine. But the changes of nozzle openings have significant influence on the flow field structure of downstream radial turbine. To evaluate this effect, the leakage flow through nozzle clearance in various nozzle openings were simulated by unsteady computational fluid dynamic (CFD). Meanwhile, the interaction between nozzle clearance leakage flow and nozzle wake were investigated to reveal its effects on aerodynamic losses and forced responses for downstream rotor. The results showed that the changes of nozzle openings not only affect the interaction between nozzle leakage flows and wake significantly, but also affect aerodynamic performance of the rotor and the blade forced response. With the decreases of nozzle openings, the nozzle leakage flow increases and the interaction between nozzle leakage flow and wake enhances. As a result, the mixing loss between nozzle leakage flow and wake increase significantly, thus enhances the pressure fluctuations in rotor blade leading edge, which intensifies the forced response of the rotor blades. This effect increases the risk of high cycle fatigue fracture caused by aerodynamic excitation on the leading edge of rotor.