Human error is an important risk factor for flight safety. Although the human error assessment and reduction technique (HEART) is an available tool for human reliability derivation, it has not been applied in flight safety assessment. The traditional HEART suffers from imprecise calculation of the assessed proportion of affect (APOA) because it heavily depends on a single expert's judgment. It also fails to provide remedial measures for flight safety problems. To overcome these defects of the HEART, this study proposes an integrated human error quantification approach that uses the improved analytic hierarchy process method to determine the APOA values. Then, these values are fused to the HEART method to derive the human error probability. A certain flight task is completed to assess human reliability. The results demonstrate that the proposed method is a reasonable and feasible tool for quantifying human error probability and assessing flight safety in the aircraft manipulation process. In addition, the critical error-producing conditions influencing flight safety are identified, and improvement measures for high-error-rate operations are provided. The proposed method is useful for reducing the possibility of human error and enhancing flight safety levels in aircraft operation processes.