Multiscale energy and mass transport processes constitute the fundamental scientific foundation for sustainable geo-energy development and carbon neutrality. This perspective synthesizes cutting-edge advances in the field into three transformative thematic areas: thermodynamically consistent pore-scale modeling with robust numerical schemes that embed fundamental physical laws into mathematical formulations; molecular-scale insights and data-driven acceleration techniques bridging nanoscopic interfacial phenomena to reservoir-scale engineering; and coupled multiphysics-artificial intelligence frameworks for hydrogen infrastructure safety and supercritical CO₂ geothermal systems. Recent research reveals a paradigm shift toward living digital twins that integrate rigorous mathematical physics, multiscale computing, and artificial intelligence, charting a clear course toward carbon-neutral energy systems.