In this paper, the paraffin section technique and optical microscopy were used to compare the morphological and anatomical structure of Taxus chinensis under the soil and hydroponic conditions. Results showed that hydroponic Taxus chinensis formed a large root system composed of a large amount of adventitious roots. The new adventitious air root had a slenderer appearance, more closely arranged epidermis, an obvious stratum corneum, and an intensive cover of slender adventitious root, while the aquatic root had a thick appearance, an unclear stratum corneum of epidermal cell wall, and thin and short root hairs. The aquatic root cortical cells had a little bit more layers than the adventitious root cells. The central vascular cylinder, the primary xylem and primary phloem bundle number of adventitious root and aquatic root were similar to the root in the soil with the bundle number being 2, but adventitious root and aquatic root had less cells and an obvious simple structure. Compared to the root in the soil, the secondary growth of hydroponic Taxus chinensis root occurred later and the secondary growth and the secondary structure were both relatively weak. The epidermis was replaced by two layers of periderm after the epidermis fell off, while the cortex was kept for a long time.