Little is known about how the COVID-19 pandemic will comprehensively affect prevalence of cigarette and e-cigarette smoking. Through a post-hoc secondary analysis from a nationwide, long-term serial, and representative study of 1.2 million individuals, the prevalence of traditional smoking decreased less than expected during the pandemic; however, that of e-cigarette smoking decreased. Our results provide an improved epidemiological understanding of smoking status before and during the COVID-19 pandemic, and suggest that more individualized and precise strategies to prevent and quit smoking are needed to improve public and global health during the pandemic.