In recent years, progress has been made in the research on the dynamic optical regulation and multi-scenario adaptability of biomimetic materials. Chameleons or lizards are commonly used biomimetic objects for color-changing or thermostatic materials. Previous studies primarily focused on analyzing the color characteristics of lizards, such as dynamic color changes and pigment distribution in response to various factors (e.g., temperature and background). However, the structure of purine crystals within iridophore cells and their specific role in body color modulation remain poorly understood. In this study, Anolis carolinensis—a lizard capable of rapid body color changes—was selected as the experimental subject. First, reflectance measurements (300–700 nm) were conducted on different body regions (head and dorsum). Subsequently, paraffin sectioning, transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were employed to quantitatively analyze purine crystals in the skin of these regions. Reflectance data revealed significant differences between the head and dorsum, with the head exhibiting significantly lower reflectance than the dorsum. Histological analysis using paraffin sections revealed a distinct cellular organization in lizard skin: xanthophore clusters were observed in the superficial layer, with iridophore aggregations directly beneath them, and melanophores positioned in the deepest stratum. When the skin color changes from green to brown, the melanin can migrate to the area above xanthophores, resulting in a brown skin coloration. TEM analysis showed that the purine clusters in the iris layer exhibited a relatively uniform but regionally concentrated arrangement, forming a unique ultrastructural pattern in the lizard skin. Further examination of crystals extracted from iris cells using SEM revealed lumpy or short columnar structures that were often stacked on top of each other, with facet diameters of 172.46 ± 29.67 nm and particle sizes of 95.30 ± 13.13 nm. Significant differences in crystal size were observed between the head and dorsum, with the dorsolateral lens being thicker and the facet diameter larger than the crystals of the head. These findings suggest that differences in crystal structure and size in different parts of A. carolinensis affect the reflectivity of the skin and thus cause differences in reflectivity. This study provides a scientific basis for further understanding the mechanism of color-changing in ectotherms, and lays a theoretical foundation for the design and manufacture of functional materials such as dynamic color-changing or high-sensitivity optical sensing.