To study the morphological and quantitative characteristics of the xylem and histochemistry of differentaged stems in Aquilaria sinensis, the anatomical structure of the stem was analyzed using the Jeffery method, histochemical staining, and microscopic observation. The results showed that the xylem was composed of 5 parts: pith, included phloem, xylem rays, vessels, and fiber tracheids. A transverse section showed that the included phloem (foraminate type) evenly distributed in the xylem. The xylem rays belonged to heterogeneous Ⅲ. The vessel pores were generally arranged as follows: radial pore clusters (2 to 4), multiple pores, pore chains (5 to 10), or a single pore; vestured pits were alternately arranged in the vessels′ lateral walls. Acclivitous simple vestured pits were present in the lateral walls of the fiber tracheid. Trabeculae were present in the neighboring fiber tracheids of the pith. Embolisms were present in the vessels and the fiber tracheids. Trabeculae and embolisms were firstly observed in A. sinensis. The levels and storage tissues of starch, reducing sugars, and volatile constituents were significantly different in the differentaged xylem. This study provides basic anatomical evidence for agarwood formation.