To study the clinical effects of Prescription Zhuyun-III (ZYIII) on early pregnant women diagnosed as threatened abortion, and its mechanism in immunity and endocrine by determining serum Th1- and Th2-type cytokines, progesterone, and beta-human chorionic gonadotropin (beta-HCG). The treatment group comprised 30 early pregnant women diagnosed as threatened abortion of deficiency syndrome of Pi, Shen, or both. The control group consisted of 20 normal early pregnant women of similar gestational age. Patients in the treatment group were administered with ZYIII for 4 weeks. Peripheral blood samples were collected pre- and post-treatment from both the treatment and the control groups. Serum Th1-type cytokine [interleukin-2 (IL-2)] and Th2-type cytokine [interleukin-10 (IL-10)] were determined by flow cytometry, and serum progesterone and beta-HCG were determined by ELISA. (1) The treatment was effective in 26 and ineffective in 4 patients of the treatment group. Therefore, the cure percentage was 86.67%. (2) In the treatment group before the treatment, IL-2 was significantly higher, IL-10 tended to be less, and the Th1/Th2 balance shifted toward Th1 compared with those in the control group. (3) After the treatment, IL-2 was decreased, IL-10 was increased, and IL-2/IL-10 was decreased. Both progesterone and beta-HCG were increased. Changes of progesterone were positively correlated with changes of IL-10, whereas changes of beta-HCG were negatively correlated with changes of IL-2. Our study suggests that ZYIII has an evident function of protecting the fetus, and one of its mechanisms is inhibiting the secretion of Th1 cytokines, promoting the secretion of Th2 cytokines, and recovering the pathological shift of the Th1/Th2 balance. The other possible mechanism is increasing serum progesterone and beta-HCG concentrations. Moreover, there are some correlations between the above two effects.