Accurately and rapidly evaluated error sensitivity of actual tooth surfaces of hypoid gears can be a significant foundation for a variety of dynamic preference analysis and machine tool setting readjustments. Due to the complexity of local geometric features as well as the limitations of the data measurement on tooth surfaces of hypoid gears, automated error-sensitivity analysis for actual tooth surfaces still presents many substantial challenges. This paper presents a novel methodology for the error-sensitivity analysis of real tooth surfaces of hypoid gears. The methodology combines an error-sensitivity analysis model with a numerical analytical real tooth contact analysis (RTCA) model. The real tooth surfaces, describing local micro-geometry features on actual tooth surfaces, have been produced by 3D discrete data points reconstruction. In this method, the discrete data points on actual tooth surfaces are measured by using a coordinate measure machine (CMM). The location, size, and shape of contact patterns are determined from the predicted interference areas distribution by numerical analysis. In addition, the error-sensitivity analysis model is established for evaluation of the sensitivity of hypoid gears with real tooth surfaces that corresponds to misalignments. The results of experiment show that the proposed method can obtain actual contact properties that significantly improve the basic design performances significantly.