The first-stage rotor squealer tip is a key area in gas turbine for both aerodynamic performance and blade cooling tasks, which should be carefully designed. However, harsh operating conditions near the rotor squealer tip can cause the geometry of the squealer tip to degrade, and manufacturing inaccuracies can also cause the squealer tip geometry to deviate from the ideal design. These geometry deviations would change the flow field near the blade tip, which will influence the thermal and aerodynamic performance. Thus, it is important to quantitatively investigate the effects of squealer tip geometry deviation on the aerothermal performance. In this paper, a typical transonic first-stage turbine is employed, and three important geometric features of squealer tip, the tip clearance height (H), the squealer depth (D), and the squealer edge chamfer (R), are selected. An uncertainty quantification process is performed to study the effect of deviation of H, D, and R on the aerothermal performance. Many cases with different geometry features are checked in the current study using 3D Reynolds-averaged Navier–Stokes simulations. A parameter sensitivity analysis using Sobol Indice method is carried out to identify the key parameters to aerothermal performance of the squealer tip. The uncertainty quantification results show that the existence of the tip chamfer reduces the size of separation bubble and the dwelling range of the scraping vortex, thus, the blockage effect of the leakage flow is weakened, which results in larger amount of leakage flow and more mixing loss of squealer tips with edge chamfer than those without edge chamfer. The results of the parameter sensitivity analysis show that the height of tip clearance is the main factor that affects the aerodynamic performance of the squealer tip. This work provides a certain guiding direction for the optimization design of the turbine groove tip.