Objective: To explore the nature of deficiency in spleen-yin syndrome, which could provide scientific theoretical support and practical guidance for clinical Traditional Chinese Medicine (TCM) syndrome differentiation based on biology, and had a strong clinical significance. Methods: Serum Cu and Zn were detected by atomic absorption spectrophotometer, serum vitamin E by high performance liquid chromatography, serum vitamin C by 2,4-Dinitrophenylhydrazine Colorimetry, total superoxide dismutase (SOD) and Cu and Zn-SOD by the xanthine oxidase method, and malondialdehyde (MDA) by the 2-thiobarbituric acid method (TBA). Total antioxidant capacity was detected by a colorimetry kit. Amylase Activity was detected by an automatic biochemical analyzer. Lysozyme was detected by lysozyme detection plate, the diameter of bacteriolysis circle was measured and the corresponding content of lysozyme was obtained from a table of standard curve values. Results: No significant difference in total SOD and Cu, Zn-SOD was found between deficiency in spleen-yin group and normal group. However, such factors in deficiency in kidney-yin group were significantly lower than the other groups (P < 0.05). The MDA content in both deficiency in spleen-yin group and deficiency in kidney-yin group were significantly higher than that of normal group (P < 0.05), while the total antioxidant capacity was significantly lower than normal group (P < 0.05). The vitamin E content in deficiency in kidney-yin group was significantly lower than that in the other two groups (P < 0.05). No significant difference in the contents of vitamin C, Cu and Zn were observed in these groups. The Zn/Cu level in deficiency in kidney-yin group and the vitamin E level in deficiency in spleen-yin group decreased, but with no significant difference. Amylase activity in unit time in cases with deficiency in spleen-yin was lower than and had significant differences with that in normal cases, and higher than that in cases with deficiency in kidney-yin. The sectional velocity of saliva and the ratio of lysozyme in normal case group were significantly higher than other two groups, while deficiency in the spleen-yin group was significantly higher than the deficiency in kidney-yin group. Conclusion: All the results indicated that the objective pathological mechanism between the deficiency in spleen-yin and deficiency in kidney-yin was different.