Twist angle errors along the blade radial direction are uncertain and affected by cutting force, tool wear, and other factors. In this paper, the measured twist angle errors of 13 sections of 72 rotor blades were innovatively analyzed to obtain the rational statistical distribution. It is surprisingly found that the under-deflection systematic deviation of twist angle errors shows a gradually increasing W-shaped distribution along the radial direction, while the scatter is nearly linear. Logically, the statistical model is established based on the linear correlation of the scatter by regression analysis to reduce variable dimension from 13 to 1. The influence of the radial non-uniform twist angle errors’ uncertainty on the aerodynamic performance of the three-dimensional compressor rotor is efficiently quantified combining the non-intrusive polynomial chaos method. The results show that the mean values of mass flow rate, total pressure ratio, and isentropic efficiency at the typical operating conditions are lower than the nominal values due to the systematic deviation, indicating that the under-deflection twist angle errors lead to the decrease in compressor thrust. The compressor’s stable operating range is more sensitive to the scatter of twist angle errors, which is up to an order of magnitude greater than that of the total pressure ratio and isentropic efficiency, indicating the compressor’s safe and stable operation risk increases. Additionally, the flow field at the tip region is significantly affected by twist angle errors, especially at the shock wave position of the near-stall condition.