The invention discloses an aircraft overall configuration hierarchical optimization method based on a multi-performance index system, which comprises a step that establishing an overall configuration multi-performance index system; wherein the index system comprises the following indexes: lift-drag ration, lift coefficient, longitudinal stability, yaw stability and rolling stability. The aircraft overall configuration optimization model is built according to the multi-performance index system; wherein the optimization model comprises an expected value of the index performance of each index in the index system. The aircraft overall configuration is hierarchically optimized of the multi-performance index, according to the optimization model, until the index performance of all indexes is capable of satisfying the expected value corresponding to each index. Through the aircraft overall configuration hierarchical optimization method, the high-speed aircraft overall configuration is optimized under the condition of strong coupling of multi-performance indicators, and the reliability of the optimization and optimization efficiency are improved.