Inflammatory bowel disease (IBD) is a chronic disease that is increasingly being recognized globally. IBD is difficult to cure and is in urgent need of more treatment options. Flos lonicerae polysaccharide (FLP) is an effective component extracted from traditional Chinese medicine flos lonicerae, and previous studies have demonstrated its therapeutic potential in treating inflammatory diseases such as rhinitis and dermatitis, but there has been few in-depth research on their regulation of IBD repair mechanisms. This study focuses on the regulatory mechanisms of FLP on the structure of the gut microbiome and immune homeostasis. Results have demonstrated that treatment with FLP effectively attenuates weight loss, reduces the release of proinflammatory cytokines, and restores spleen and colon structures in mice. These effects are achieved through modifying the intestinal microbial community structure, increasing beneficial bacteria, and decreasing harmful bacteria. Furthermore, FLP significantly impacts the levels of Coenzyme Q2, a lipid closely associated with mitochondrial function. This modulation possibly regulates oxidative stress levels and the NF-κB pathway, thereby contributing to the alleviation of IBD. Therefore, FLP as a natural product with multiple biological activities, exhibits potential therapeutic effects in regulating intestinal microbiota, reducing oxidative stress, and inhibiting the NF-κB pathway, suggesting it may serve as a novel strategy for IBD treatment.