Objective To study the effect of Huatan Chushi Decoction on the ultrastructure of thymus cortex and oxidative damage in aging rats. Methods A total of 40 Wistar rats (weighing 130-170 g) were randomly divided into normal control group, aging group, decoction group and positive control group, with 10 rats in each group. After receiving subcutaneous injection at nape of neck with 1 ml/(kg·d) normal saline in the normal control group and 48 mg/(kg·d) D-galactose in the other 3 groups, the rats of above groups were gavaged distilled water at 10 ml/(kg·d) in the former 2 groups, 20 g/(kg·d) decoction in the decoction group, and 0.3 g/(kg·d) vitamin E solution in the positive control group. At the end of 40 days′ intervention, all rats were sacrificed, and the contents of total antioxidation capacity (T-AOC), lipid peroxide(LPO) and lactate dehydrogenase (LDH) in the serum were detected. The ultrastructure of thymus cortex was observed with transmission electron microscopy. SPSS statistics 20.0 was used to perform the statistical analysis. One-way analysis of variance was applied for multi-group comparison, and Bonferroni test for comparison between groups. P<0.05 was regarded as statistical significance. Results The body mass of rats in each group was increased significantly on the 14th, 28th and 41st days, and the growth rate was slightly lower in the decoction group than the other 3 groups, but there was no significant difference among the groups (all P>0.05). On the 41st day, the T-AOC level was significantly lower while the contents of LDH and LPO were obviously higher in the aging group than the control group (P<0.01). The T-AOC level was remarkably increased while the content of LDH was notably decreased in the decoction group and positive control group than the aging group (P<0.05). The serum LPO content was decreased in the decoction group and the positive control group, but statistical difference was only seen in the former group (P<0.01). The decoction group had higher T-AOC level but lower LPO content when compared with the positive control group (P<0.01), but no such difference was observed in the content of LDH (P>0.05). In the aging group, the epithelial cells and lymphocytes in the thymus cortex were significantly reduced, and displayed obviously destroyed cell structure, with shrunk and deformed nucleus, decreased mitochondria, endoplasmic reticulum and other organelles and increased lysosomes in the cytoplasm. The decoction group and the positive control group showed larger numbers of epithelial cells and lymphocytes in the thymus cortex and obviously improved cell structure when compared with the aging group. Conclusion The decoction can improve the body′s antioxidant capacity, reduce oxidative damage and accumulation of oxidative products, increase the numbers of epithelial cells and lymphocytes in the thymus cortex, and protect cell morphology and mitochondrial ultrastructure. Huatan Chushi Decoction has an intervening anti-aging and immune function