<p>Halloysite nanotubes (HNTs), naturally occurring aluminosilicate nanotubes characterized by intrinsic hollow architectures and asymmetric inner–outer surface chemistry, have emerged as promising nanocontainer platforms for controlled molecular transport and delivery. This review provides a systematic analysis of the structural foundations and interfacial engineering strategies that enable HNTs to function as programmable nanocarriers in advanced materials systems. Particular attention is devoted to the multiscale structural characteristics of HNTs, surface modification approaches, and pore regulation strategies that govern loading capacity and transport pathways. Recent advances in stimuli-responsive systems are critically discussed, including pH-, temperature-, light-, and redox-responsive release mechanisms, together with their associated kinetic models describing confined mass transport. Through interfacial functionalization and the construction of polymeric or molecular gating structures, passive diffusion processes can be transformed into signal-regulated release behaviors with tunable kinetics. These mechanisms underpin the broad applicability of HNTs-based nanocontainers in diverse fields such as biomedicine, food packaging, agriculture, and corrosion protection. Finally, current challenges and emerging opportunities are highlighted, including improved structural controllability, quantitative understanding of nanoscale transport mechanisms, scalable functionalization strategies, and long-term biosafety evaluation. Advancing these aspects will be essential for translating HNTs-based nanocontainer systems from laboratory studies toward practical materials engineering applications.</p>