The next generation of human-rated space vehicles will need to keep humans alive further fromEarth than ever before. This prospect introduces many unique challenges including issues with logistics, communications, and safety. The nature of deep-space habitation will necessitate a level of vehicle autonomy not yet realized for human-rated spacecraft. This work proposes that Digital Twin technology can be used as a new tool to enable heightened autonomy and situational awareness that will ensure the safety of the vehicle and its crew. Use-cases specific to deep-space habitation are explored in detail. A Digital Twin Framework capable of supporting deep-space habitat autonomy is proposed and applicable engineering requirements are established. A demonstration implementation is proposed as a proof of concept to show the basic functioning and utility of the proposed Digital Twin. This study found that a Digital Twin is a necessary and enabling piece of technology for future human-rated spacecraft venturing into deep-space. Necessary future research targets are identified including reducedorder system-of-systems modeling, cross-scale coupling of models, integrated model verification and validation, and semantic interoperability that allows clear communication of any data, information, or query between the Digital Twin and its users.