Extending urban development underground has become a natural choice in response to land resource constraints and limitations on sustainable development. The construction of underground eco-cities is directly driven by national strategies such as those for deep-Earth and deep-space exploration, and aligns with major needs such as coping with extreme environments. Conventional underground development models are characterized by single functionality, rigid morphology, and insufficient ecological circulation capacity, making them inadequate to support emerging demands. There is a pressing need to research new paradigms and formulate their development pathways. Based on a systematic understanding of the development context of underground eco-cities and an analysis of key research breakthroughs, this study proposes a new paradigm for constructing underground eco-cities based on the concept of cross-scale bionics. It precisely analyzes the micro-geometric morphology and mechanical mechanisms of ant nests, revealing their excellent mechanisms in stress management, energy consumption optimization, and system synergy. Core design principles at the meso-scale, such as resilience, sustainable circulation, and distributed intelligence, are identified and then mapped onto the macro-scale functional topological structure and deep stress-adaptive morphology of underground cities. Guided by this methodology, a three-dimensional strategic blueprint for a depth-scalable, morphologically adaptive underground eco-city is constructed. Based on cutting-edge engineering practices both in China and abroad, it is preliminarily judged that the pathway from biological wisdom to engineering practices is viable. For future applications, key enabling technologies across the entire chain of "perception–modeling–regulation–decision-making" and developmental elements like synergistic "legal–social–economic" management are elaborated. This study will directly promote a fundamental shift in underground development from passive adaptation to active shaping. The new paradigm proposed possesses both universality and good transferability, providing theoretical references for serving deep space strategies and constructing subsurface habitats on extraterrestrial celestial bodies.