We aimed to establish the prevalence of atypical masturbation in the general population and explore the association between atypical masturbation and male sexual dysfunction in heterosexual males. Atypical masturbation refers to stimulation significantly distinct from that encountered during partnered sexual activity. We posted questionnaires that contained the abridged International Index of Erectile Function (IIEF-6) and the premature ejaculation diagnostic tool on social media in China. We collected 2743 valid questionnaires from December 9, 2020, to April 18, 2021. We found that the prevalence of atypical masturbation in the general population was 10.97%. Men with atypical masturbation had lower IIEF-6 scores and higher rates of erectile dysfunction (ED) than men with typical masturbation. The prevalence of premature ejaculation and estimated intravaginal ejaculatory latency time were not significantly different among men with different patterns of masturbation. Our study demonstrated that atypical masturbation is associated with ED, and a clinician dealing with sexual issues should inquire more fully about masturbation patterns than has been done to date.