Heated tobacco products (HTPs) have been widely used in Korea since their introduction in 2017. In this study, we investigated the perceptions of their relative harmfulness and smoking cessation effects. We performed an online survey in 7000 Koreans in 2018 (2300 males and 4700 females aged 20–69 years) by matching their age, sex, and provincial distribution. To investigate the factors causing HTPs to be perceived as less harmful than combustible cigarettes (CCs) and helpful for smoking cessation, we used multivariable logistic regression analyses. HTPs were less harmful than CCs in 16.8% of participants, particularly among HTP-only users and dual and triple users of HTPs, electronic cigarettes (ECs), or CCs than among CC-only users, those who were aged ≤ 34 years, males, and those with higher incomes. HTPs were reportedly helpful for smoking cessation in 11.2% of participants. Similar perceptions were more likely among HTP-only users, as well as dual and triple users than among CC-only users and adults with higher education/incomes. Although Korean adults generally had negative perceptions of the harmfulness and smoking cessation effects of HTPs compared with CCs, dual and triple users were more likely to have positive perceptions. Monitoring the use of multiple tobacco products and HTPs is a new challenge for Korean policymakers.