The transonic high-pressure turbine is a critical component in modern aviation engines which is susceptible to geometric variations throughout its entire lifecycle. However, the specific impact and underlying mechanism of geometric deviations on the performance are not yet fully understood. This article presents a framework for modeling, quantifying, and analyzing geometric variations in typical transonic high-pressure turbines. It aims to investigate the mechanism by which geometric variations impact aerodynamic performance across the entire operating range. Additionally, the study explores potential improvement methods for controlling the adverse effects caused by geometric deviations. The results indicate that within the entire operating range, the trailing edge and throat have the greatest impact on the fluctuation of total pressure loss. Deviation in the trailing edge and throat directly impacts the range of the base region and base pressure, leading to changes of shock waves and wake flow. This causes fluctuations in shock wave loss and trailing edge loss, ultimately resulting in the fluctuation of total pressure loss. Subsequently, two methods were proposed to suppress the influence of geometric deviations: the utilization of an elliptical trailing edge and a specially designed throat profile. These approaches effectively reduce the loss fluctuations caused by geometric deviations, particularly under typical transonic conditions.