According to the characteristics of the heterogeneous unmanned aerial vehicle (UAV) formation cooperative task assignment in the anti-radar combat, an improved mixed integer linear program task assignment algorithm which takes the time window in to account, is proposed. Specifically, the reasonable variable definition and collaborative constraints between UAVs and the tasks are presented in detail. On the other hand, since the genetic algorithm has advantages of global search ability and parallel computing ability, a timewindow based multi-layer coding genetic algorithm is proposed too. The simulation and analysis show the proposed algorithms are available for the anti-radar cooperative combat, and the related advantages and applicability of the presented algorithms are analyzed too.