The endemic Metasequoia glyptostroboides Hu & Cheng 1948 (Cupressaceae), the Dawn Redwood, is the only extant representative of the Metasequoia genus which has an abundant fossil record in the Northern Hemisphere since the Cretaceous. With only a small native population restricted to south-central China, the Dawn Redwood is facing serious challenges today due to its low genetic diversity, urbanization, and climate change, although cultivated trees have thrived around the globe. Metasequoia has been used as a model taxon for studies in paleobotany, paleoecology, and paleoclimatology, drawing on data from its extensive fossil record, cuticular micro-morphology, biomolecules, stable isotope signals, etc. Two types of cuticles, the even type and the uneven type, have been characterized in its native living population with the vast majority of trees having uneven type cuticles. The even type is rarely found: From only a single tree in Paomu Village, Luota Town, Longshan County, Hunan Province, China (the “Paomu Tree”) and occasionally from some high branches of mature trees or juvenile seedlings. However, fossils all over the world are represented by the even type cuticle except for two recent reports of the uneven type in Miocene fossils from Yunnan and Inner Mongolia in China. Competing hypotheses exist regarding the origin and relationship of these two cuticular types—whether they were caused by genetic mutation(s), different ecological conditions or combined influences. Ultimately, the resolution of this question will have critical implications in the conservation plan for this living fossil species and the application of its cuticular features for paleoecology and paleoclimate research. Metasequoia’s thin and uneven type cuticle is notorious for being difficult to prepare in order to recover large pieces for accurate measurements of cell dimensions. The development of a cleared leaf epidermis (CLE) technique, modified from the conventional cleared leaf method solved the problem by obtaining a complete and transparent epidermal layer, allowing accurate measurements of three-dimensional epidermal features in both types of both fossil and modern Metasequoia. By applying this method to fossil leaves from the mid-Miocene Clarkia deposit in Idaho and various modern leaves, we carried out a statistical comparison of guard cell size and geometry of Metasequoia. Our data indicates that fossil leaves have relatively smaller guard cells compared with their living relatives, but the range of the two groups are still overlapping, implying that guard cell size is related to taxonomy and likely influenced by atmospheric CO2 levels as the Miocene Metasequoia lived under much higher CO2 conditions. Through pyrolysis analysis of various conifer fossil compressions with different levels of preservation, we demonstrated that the CLE technique is readily applicable to other plant taxa for both modern and fossil specimens. We believe its wide usage can solve a variety of botanical and paleobotanical issues which bear conservation and paleoclimate applications.