In the design of hypersonic cruise vehicles, great effort is demanded to improve the performances of subsystems, namely structure, aerodynamics, and propulsion. Herein, effort demanded to realize a subsystem performance is quantified by technical merit. To achieve a feasible design, excessive technical merit of any one subsystem should be avoided. Accordingly, a lowest-technical-merit (LTM) ... [Show full abstract] design methodology has been proposed in this work. By this methodology, the design problem could be interpreted into a parametric optimization. The solution to such an optimization corresponds to the highest feasibility. The methodology has been implemented on two cases: deriving a hydrocarbon-fueled long-range cruiser from Boeing X-51A, and a hydrogen-fueled LAPCAT scenario from PREPHA. The simulation results show that LTM could achieve the optimal allocations while satisfying different payload/range performances. The design methodology could help to improve the feasibility of hypersonic cruise vehicles. Furthermore, it could also be used in design of other systems.