Abstract: To improve the flight test efficiency by designing test points, this paper develops the optimal flight test design method based on discrete optimization. This study establishes an aero-engine performance thrust model by quantizing the effects of different variables on the thrust model based on the significance test, and removing those insignificant variables. The D-optimal is first used to evaluate the quality of the test point combination. Then the test point discrete optimization is performed with an adaptive genetic algorithm whose encoding process is replaced by the test point combination, such that the optimal test point combination is obtained under the test constraint. The discrete optimization based test design method is applied for the aero-engine performance flight test, and the results show that: The optimization is not only related to the test point distribution, but also related to the number of test points. When the initial number of the optimal test point combination is 12, the max error of the thrust model is 2.45%; when the final number of the optimal test point combination is 23, the max error of the thrust model is less than 0.81%. The present method can obtain the optimal test point combination effectively, improve the accuracy of the thrust model, and meet the requirements of engineering applications.