Benign prostatic hyperplasia (BPH) is a common and frequently occurring disease in clinics, with the main manifestations including frequent micturition, urinary incontinence, dysuria, and endless urination. Transurethral resection of the prostate (TURP) is the main treatment for BPH, but some patients are prone to urinary tract infection after surgery, which affects the prognosis. Therefore, it is of great significance to study the pathogenic characteristics and risk factors of postoperative urinary-derived pathogenic bacteria infection in patients with BPH for the prevention and treatment of postoperative infection. In addition, the treatment of patients with this disease is also the focus of clinical attention. Long-term massive application of antibiotics can induce drug-resistant mutations of bacteria, so it is urgent to find an efficient and safe therapeutic scheme in clinics. However, traditional Chinese medicine (TCM) has a long history of treating urinary tract infections. Therefore, Shuangdong capsule, a traditional Chinese medicine preparation, was selected for the combined treatment in this study. The results showed that age, concomitant diabetes mellitus, and preoperative prophylactic application of antibiotics were the independent risk factors for postoperative urine-derived pathogenic infection in BPH patients. Clinical intervention for BPH patients with concomitant risk factors should be emphasized in clinical practice. The combined use of Shuangdong capsule and conventional western medicine can improve the clinical symptoms and inflammatory reactions of postoperative urine-derived pathogenic infection in BPH patients. Due to its exact curative effect and high safety, it is worthy of promotion. The clinical study registration number is M2022019.