As the variable nozzle turbine (VNT) becomes an important element in engine fuel economy and engine performance, improvement of turbine efficiency over wide operation range is the main focus of the research efforts for both the academia and industry in the past decades. It is well known that in a VNT, the nozzle endwall clearance has big impact on the turbine efficiency, especially at small nozzle open positions. However the clearance at hub and shroud wall side may contribute differently to the turbine efficiency penalty. When total height of nozzle clearance is fixed, varying distribution of nozzle endwall clearance at hub and shroud sides is possible to generate different patterns of the clearance leakage flow that has different interaction with and impact on the main flow after exiting the clearances. It is possible that variation of the nozzle endwall clearances between hub side and shroud side, e.g. tiny spanwise movement of nozzle vanes along their pivotal shafts, has resulted in significant deviations in turbine aerodynamic performances. In this paper, the deviations of turbine efficiency at three different nozzle vane openings and different rotation speeds, with different distribution of nozzle endwall clearances were numerically analyzed. It was found that when the total height of nozzle clearances is fixed, changing the nozzle endwall clearance distribution between the hub and shroud sides can improve the turbine efficiency. Nozzle endwall clearance at shroud side, especially at low turbo speed and small vane open positions, seem to have more impact on the turbine efficiency.