Lower urinary tract symptoms (LUTS) are substantially prevalent and increase with age. Research on smoking as a risk factor for LUTS has been inconclusive. The present study examined the association between smoking habits and male LUTS in a population-based study using a web-based questionnaire. We firstly screened a total of 10,000 male participants who were selected according to the age distribution in the Japanese population in government data, in order to check smoking habits. We then performed a web-based survey to further investigate factors associated with LUTS, using the Overactive Bladder Symptom Score (OABSS), International Consultation on Incontinence Questionnaire-Short Form (ICIQ-SF), and International Prostate Symptom Score (IPSS) questionnaire. Finally, 9042 participants (non-smokers, n = 3545; ex-smokers, n = 3060; and current-smokers, n = 2437) completed the full continence survey. Current-smokers (2.54 ± 2.73, 1.98 ± 3.57, 5.75 ± 7.02) and ex-smokers (2.80 ± 2.52, 1.81 ± 3.10, 6.58 ± 6.96) showed significantly higher OABSS total, ICIQ-SF total, and IPSS total scores than non-smokers (1.98 ± 2.40, 1.35 ± 2.90, 4.23 + -/6.33) (p: < 0.0001, < 0.0001, < 0.0001, respectively). In comparison to non-smokers, the prevalence of risk ratio for day-time frequency, nocturia, urgency urinary incontinence (UUI), OAB, and IPSS ≥ 8 were 1.2 1.2 1.4 1.5 1.5, respectively, in current-smokers and 1.3, 1.5, 1.5, 4.5, 1.8 in ex-smokers. The relative risk of OAB, nocturia, UUI, and IPSS ≥ 8 in ex- and current-smokers in comparison to non-smokers was high in the young age groups in comparison to the elderly groups. Current-smokers and ex-smokers showed a higher prevalence of male LUTS. This phenomenon was highly observed in relatively young age groups.