This thesis addresses the challenges associated with thermal management systems (TMS) evaluation and selection in the conceptual design of hypersonic, air-breathing vehicles with sustained cruise. The proposed methodology identifies analysis tools and techniques which allow the proper investigation of the design space for various thermal management technologies. The design space exploration environment and alternative multi-objective decision making technique defined as Pareto-based Joint Probability Decision Making (PJPDM) is based on the approximation of 3-D Pareto frontiers and probabilistic technology effectiveness maps. These are generated through the evaluation of a Pareto Fitness function and Monte Carlo analysis. In contrast to Joint Probability Decision Making (JPDM), the proposed PJPDM technique does not require preemptive knowledge of weighting factors for competing objectives or goal constraints which can introduce bias into the final solution. Preemptive bias in a complex problem can degrade the overall capabilities of the final design. The implementation of PJPDM in this thesis eliminates the need for the numerical optimizer which is required with JPDM in order to improve upon a solution. In addition, a physics-based formulation is presented for the quantification of TMS safety effectiveness corresponding to debris impact/damage and how it can be applied towards risk mitigation. Lastly, a formulation loosely based on non-preemptive Goal Programming with equal weighted deviations is provided for the resolution of the inverse design space. This key step helps link vehicle capabilities to TMS technology subsystems in a top-down design approach. The methodology provides the designer more knowledge up front to help make proper engineering decisions and assumptions in the conceptual design phase regarding which technologies show greatest promise, and how to guide future technology research.