Objective To investigate the clinical effect of granules for tonifying the kidney and preventing miscarriage combined with dydrogesterone in the treatment of early threatened abortion with kidney deficiency and its effect on the levels of stromal cell derived factor-1α(SDF-1α) and matrix metalloproteinase-9(MMP-9). Methods A total of 60 patients with early threatened abortion with kidney deficiency were randomly divided into treatment group and control group, with 30 patients in each group. The patients in the treatment group were given oral granules for tonifying the kidney and preventing miscarriage combined with dydrogesterone, and those in the control group were given oral dydrogesterone; the course of treatment was 2 weeks for both groups. The two groups were compared in terms of traditional Chinese medicine (TCM) symptom score before and after treatment and overall response after treatment, and ELISA was used to measure the changes in the levels of SDF-1α and MMP-9. Results The treatment group had significantly better overall response than the control group (P<0.05). After treatment, both groups had significant reductions in total TCM symptom score and the scores of vaginal bleeding time and bleeding volume (P<0.05), and the treatment group had significant reductions in the scores of lower abdominal pain or bulge, lumbago, dizziness and tinnitus, frequency of nocturia, and soreness and weakness of both knees (P<0.05). Compared with the control group, the treatment group had significantly greater reductions in total score and the scores of all symptoms except bleeding volume (P<0.05). The treatment group had significant increases in the levels of SDF-1α and MMP-9 after treatment (P<0.05), and the treatment group had significantly greater increases than the control group (P<0.05). Conclusion Granules for tonifying the kidney and preventing miscarriage combined with dydrogesterone has a marked clinical effect in the treatment of early threatened abortion with kidney deficiency and can improve patients clinical symptoms and quality of life, possibly by upregulating the levels of SDF-1α and MMP-9 and correcting angiogenesis disorder at the maternal-fetal interface.