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2D clay minerals have advantages in subnanometer interlayer space, rich surface chemistry, light transparency and low cost for mass production, which enable their applications in mass separation, smart optics, and energy conversion devices. Over the past 30 years, significant progress has been made on scalable fabrication and high-value applications of natural clay minerals-based two-dimensional (2D) materials. Natural clay minerals-based 2D materials have layered structures, high ion conductivity and selectivity, tunable surface charge, remarkable chemical stability, mechanical resilience, low cost and abundance in nature. Here, we provide a comprehensive review of the advances in characterizations, properties and applications of 2D phyllosilicates. First, it summarizes the fundamentals including crystal structure and ion exchange properties of 2D clay minerals. Subsequently, it highlights how advanced characterization techniques and computational methods interconnect the structure and behavior of 2D clay minerals. We then discuss the recently developed fabrication methods of 2D phyllosilicates to make them suitable for the study of intrinsic properties, as well as for scalable devices. Next, it is elaborated on how the intrinsic properties of 2D phyllosilicates such as light transparency, surface chemistry and confined interlayer space influence their applications in ion and molecular separation, energy harvesting, and liquid crystals individually or synergistically, so that the relationship of structure-properties is elucidated. Finally, the next-generation design concepts, including multi-dimensional printing strategy and smart devices, in the fabrication and application fields of 2D clay minerals are proposed.