We applied an anatomical observation of the development of stem and leaf of the endangered plant Scutellaria tsinyunensis in the method of paraffin microtomy, obtained the leaf epidermis of various stages of development to observe micromorphological features at the same time, to achieve the purpose of providing a theoretical reference for the conservation and utilization of local unique precious species resources. Results showed that: (1) the hemispherical growth cone of S. tsinyunensis, consisted of the tunica and the corpus, was the starting point of development; (2) stem development experienced of the original meristem, primary growth, secondary growth, and ultimately the formation of mature stem structure, lignification increased, the surface glandular hair loss, nonglandular hair increased; (3) leaves came from promeristem, then procuticle, ground meristem and procambium differentiated, finally mature mesophyll and veins formed. When leaves matured, the fence organization proportion was greatly reduced, and the leaf space was very large. Petiole central vascular bundle was similar to the main vein structure of the blade, and the vascular bundle at the protrusion was simplified. (4) The stomatal index of S. tsinyunensis was smaller but overall lower slightly. The stomatal density decreased firstly and then decreased gradually, and the glandular hair gradually disappeared and the nonglandular hair gradually increased.