In variable geometry turbine vanes, tip clearance height and shape vary with the rotation of the vane, which affect the aerodynamic performance significantly. However, these issues are rarely considered in published studies. The current paper investigated the flow field features of transonic variable geometry turbine vanes with non-uniform partial clearance induced by the vane rotating. The results show that: The influence of guide vane rotation on the clearance height and its distribution cannot be ignored. At the same turning angle, the maximum clearance difference is up to 0.79 mm (0.8 % vane height). The height and shape variation of the non-uniform clearance leads to the change in the leakage flow rate, secondary flow structure, and aerodynamic loss of the variable guide vane. Under the combined effect of pressure difference on both sides of the clearance, axial and circumferential non-uniformity of clearance height, the total pressure loss coefficient is up to 9.44 % when the turning angle is −10°. The effect of the pivot on the clearance flow was also analyzed. The pivot increases the pressure in the gap flow field and reduces leakage flow velocity. However, a backflow region appears at the suction side of the pivot, which increases the aerodynamic losses.