Lower urinary tract symptoms (LUTS) are strongly linked with obesity. Whether bariatric surgery can effectively alleviate LUTS in morbidly obese men is unknown. The objective of the present study was to evaluate the effectiveness of bariatric surgery in reducing the prevalence and severity of male LUTS in obese patients. This was a prospective observational study on consecutive morbidly obese men undergoing bariatric surgery. The International Prostate Symptom Score (IPSS) was used to assess for LUTS before and at 1-3 years after surgery. The 3-year changes in IPSS, the changes in LUTS severity, and the factors associated with LUTS improvement were evaluated. This study recruited 143 morbidly obese men (mean age 43.0 ± 10.4 years) undergoing sleeve gastrectomy (n = 89) and Roux-en-Y gastric bypass (n = 54). The rates of follow-up after surgery were 94.4% (n = 119/126) at 1 year, 90.6% (n = 96/106) at 2 years, and 81.2% (n = 69/85) at 3 years. After surgery, there was significant body mass index reduction from 39.1 ± 5.2 kg/m2 preoperatively to 30.1 ± 4.8 kg/m2 at 1 year and 31.5 ± 4.9 kg/m2 at 3 years (P < 0.001). There was significant reduction in IPSS total symptom score, quality of life score, frequency score, and nocturia score (P < 0.05). The prevalence of moderate to severe LUTS reduced from 35.0% (29.4% moderate; 5.6% severe) preoperatively to 21.8% (19.3% moderate; 2.5% severe) at 1 year and 30.4% (24.6% moderate; 5.8% severe) at 3 years (P < 0.001). LUTS improvement was significantly associated with body fat percentage reduction (P = 0.012) and was not associated with weight loss or improvement of metabolic parameters. Bariatric surgery was an effective and durable intervention for alleviating the prevalence and severity of LUTS in morbidly obese men for up to 3 years.