INTRODUCTION: Smoking is one of the most important predisposing factors of intestinal inflammatory diseases. Heated tobacco product (HTP) is a novel tobacco category that is claimed to deliver reduced chemicals to humans those reported in combustible cigarette smoke (CS). However, the effect of HTP on the intestine is still unknown. AIMS AND METHODS: Our study aims to explore the potential effects of HTP on intestine. In the framework of Organization for Economic Co-operation and Development guidelines 413 guidelines, Sprague-Dawley rats were exposed to HTP aerosol and CS for 13 weeks. The atmosphere was characterized and oxidative stress and inflammation of the intestine were investigated after exposure. Furthermore, the feces we performed with 16S sequencing and metabolomics analysis. RESULTS: HTP aerosol and CS led to obvious intestinal damage evidenced by increased intestinal proinflammatory cytokines and oxidative stress in male and female rats After HTP and CS exposure, the abundance that obviously changed were Lactobacillus and Turiciacter in male rats and Lactobacillus and Prevotella in female rats. HTP mainly induces the metabolism of amino acids and fatty acyls such as short-chain fatty acids and tryptophan, while CS is involved in the main metabolism of bile acids, especially indole and derivatives. Although different metabolic pathways in the gut are mediated by HTP and CS, both inflammation and oxidative stress were ultimately induced. CONCLUSIONS: HTP aerosol and CS-induced intestinal damage are mediated by different gut microbiota and metabolites, while both lead to inflammation and oxidative stress. IMPLICATIONS: The concentration of various harmful components in heated tobacco product aerosol is reported lower than that of traditional cigarette smoke, however, its health risk impact on consumers remains to be studied. Our research findings indicate that heated tobacco products and cigarette smoke inhalation induced intestinal damage through different metabolic pathways mediated by the gut microbiome, indicating the health risk of heated tobacco products in the intestine.