Due to the need of studying midcourse penetration counter simulation, the quick design method of intercept trajectory layout about Exoatmospheric Kill Vehicle(EKV) was researched. With analyzing the combat mission of interceptor. The main restric condition that the missile’s place and speed should obey in the cutoff of Ground Based Interceptor (GBI) was gave out. Take the minimum of intercept rendezvous angle as objective function, the optimal model of inverse design of intercept trajectory about EKV is established. Finally,six trajectory parameters of EKV initial trajectory and GBI initial parameters of three restrict condition are got by genetic algorithm and reverse integral method. The correctness of the strdying method is proved by the result of simulation. The method of inverse design offers a new method for missile penetration counter simulation.