Background and Objective: Calcium and vitamin D supplementation is generally the preferred treatment for abnormal bone metabolism in patients with diabetes. Alendronate is used in patients with abnormal bone metabolism but has adverse effects like headache and dizziness. Zuogui pill has established an anti-osteoporotic effect through kidney-tonifying medication. The objectives of the study were to evaluate the efficacy and safety of the Zuogui pill with calcium against daily alendronic acid with calcium and calcium alone in patients with diabetes for the management of abnormal bone metabolism. Materials and Methods: Data of demographical, clinical and pathological parameters, bone density, Visual Analog Scale (VAS) and adverse effects (9 months from start of therapy and 6 months of follow-up) of 431 patients on hypoglycemic therapy and had T-score or Z-score of lumbar spines or/and femoral bone less than -1 were collected and analyzed. Diabetic patients received 27 g Zuogui pill, 600 mg calcium carbonate and 400 IU cholecalciferol/day (ZC cohort, n = 115) or 10 mg alendronic acid, 600 mg calcium carbonate and 400 IU cholecalciferol (TC cohort, n = 135)/day or 600 mg calcium carbonate and 400 IU cholecalciferol twice in a day (CC cohort, n = 181) for 9-months. Results: After treatment (EL) T-score and Z-score of lumbar spines and femoral bone were increased in the ZC and AC cohort as compared to before treatment (p<0.05 for all). At EL T-score and Z-score of lumbar spines and femoral bone were increased for patients of the ZC cohort than those of the AC and the CC cohorts (p<0.05 for all). Only in the ZC cohort T-score and Z-score of lumbar spines bones and femoral bones of patients were increased more than -1. The VAS of patients of the ZC cohort was increased at EL than before treatment (4(2-6) vs. 3(2-5), p<0.001). Gastrointestinal discomfort, diarrhea, dizziness and fatigue were reported in the ZC cohort. Gastrointestinal discomfort, dizziness, headache, nausea, constipation, vomiting, blistering, irregular heartbeats, peeling, angioedema, numbness, difficulty with breathing, tingling effect, weight gain, hair fall, skin rash and redness of eyes with irritations were reported in the AC cohort. Conclusion: Zuogui pill with calcium effectively improves bone mineral density and pain with manageable adverse effects in diabetic patients with abnormal bone metabolism than alendronic acid with calcium or calcium alone.