Background Combustible cigarettes have detrimental effects on periodontal disease. However, little evidence is available regarding new heated tobacco product (HTP) use and combined product use (both combustible cigarettes and HTPs). This study aimed to examine the association of combustible cigarettes, HTPs, and combined product use with periodontal disease simultaneously. Materials and methods This cross-sectional study was conducted using data from the 2019 arm of the longitudinal Japan "Society and New Tobacco" Internet Survey. Combustible cigarette users, HTP users, combined product users, never-users, and former users' data were separately obtained. In the present study, the primary outcome was self-reported periodontal disease. We estimated adjusted prevalence ratios (PRs) and confidence intervals (CIs) using multivariable modified Poisson regression analysis after adjusting for 12 confounders. Results Of the 10,439 JASTIS respondents, the numbers of users of combustible cigarettes only, HTPs only, and both products were 1,304, 437, and 1,049, respectively. Compared with never-users, HTP use was significantly associated with the prevalence of self-reported periodontal diseases (PR 1.43, 95% CI 1.03-1.62). Moreover, former users, combustible cigarette users, and combined product users also showed significant associations (PR 1.56, 95% CI 1.35-1.80; PR 1.29, 95% CI 1.03-1.62; and PR 1.55, 95% CI 1.20-1.99, respectively). Conclusions Users of HTPs, combustible cigarettes, and combined products as well as former users were all significantly associated with a higher prevalence of periodontal diseases compared to never-users.