Oral cavity contains the second largest microbial community in the human body. Due to the highly vascularized feature of mouth, oral microbes could directly access the bloodstream and affect the host healthy systemically. The imbalance of oral microbiota is closely related to various oral and systemic diseases. Green tea extracts (GTE) mainly contain tea polyphenols, alkaloids, amino acid, flavones, and so on, which equipped with excellent anti‐inflammatory activities. Previous studies have demonstrated the beneficial effects of GTE on oral health. However, most researches used in vitro models or focused on limited microorganisms. In this study, the regulatory effect of GTE on oral microbiome and the alleviative effect on oral inflammation in vivo were evaluated. The results showed that GTE could efficiently alleviate the inflammations of the tongue, cheek pouch, as well as throat. GTE effectively inhibited the activation of NF‐κB through the upregulation of the anti‐inflammatory cytokine interleukin (IL)‐10, consequently leading to reduced expression of pro‐inflammatory cytokines IL‐6 and tumor necrosis factor‐α. The indexes of spleen and thymus were also elevated by GTE in stomatitis mice. Moreover, GTE promoted the growth of probiotics Lactobacillus and Bacillus, inhibited the reproduction of pathogens Achromobacter, reversing the microbiota disorders in oral cavity. This study not only presents a novel approach for enhancing oral microecology but also facilitates the wider adoption of tea consumption.