According to the design requirements related to high endurance factor, short take-off and landing , deforming resistance of MALE UAV, the investigation of the design methodology on multi-constraint of the two-element airfoil is conducted based upon the earlier studies of the one-element airfoil design. In this paper, the geometry of the two-element airfoil is generated with the method of controllable conic curves accompanied with the control points, and the parameters of control curves, slot and spin axis position are optimized using Genetic Algorithms. The results indicate that comparing to the ellipse cutting method, the present method using more control parameters is more flexible to the earlier airfoil and the pressure distributions is more reasonable. At the same time, the endurance factor, take-off lift and lift-to-drag ratio of the designed slot airfoil are improved substantially which satisfies the multi demands. This method in this paper is significant to the MALE UAV design.