Quantum radar is a novel detection method that combines radar and quantum technologies. It exceeds the detection threshold and poses a threat to conventional stealth targets. This work aims to derive the expression of the quantum radar cross-section of a new complex target. The calculation formula of QRCS was derived after introducing the relative photon parameters and vector dot product. Subsequently, a comprehensive optimization model of quantum stealth and lift–drag ratio based on a genetic algorithm was proposed for the waverider warhead. During the optimization process, we proposed an optimization method with the objective function of the QRCS pioneering design value and achieved better outcomes than the optimization method using the average value in terms of QRCS performance and lift–drag ratio in the important azimuths of the waverider. By changing the design variables of the waverider warhead and using this new optimization method, the QRCS of the waverider in the forward and lateral angles were minimized, remarkably improving the aerodynamic performance of the waverider. Similarly, the optimization results show that the proposed design value optimization method is feasible.