Objective. Meditation has been widely used for the treatment of a variety of psychological, cardiovascular, and digestive diseases as well as chronic pain. Vegetarian diets can effectively prevent hypertension, metabolic diseases such as diabetes and obesity, and certain cancers. Meditation and vegetarian diets have been recognized as components of a healthy lifestyle and have therefore attracted more people around the world. Meditation can help regulate overall health through the neural‐endocrine‐immune network. Changes in dietary habits can affect the composition of the intestinal flora, which in turn affects human physiology, metabolism, nutrition, and immune function through the bacteria‐intestine‐brain axis. Here, we aimed to investigate the effect of long‐term meditation and vegan diet on human intestinal flora. Materials and Methods. The present study used 16S rDNA sequencing technology to detect the differences in intestinal flora between 12 healthy vegan subjects receiving long‐term meditation training and 12 healthy omnivorous subjects who never received any meditation training. Results. The results showed that, compared with the subjects in the omnivorous healthy control group who had never received any meditation training, the intestinal flora structure in the people who followed the long‐term vegan meditation practices changed significantly. The intersection set between the results of the LEfSe analysis and the Wilcoxon rank sum test includes 14 bacterial genera. These 14 genera are defined as the dominant genera, and the AUC value was 0.92 in the ROC curve, which demonstrates that the 14 genera can be used as a biomarker to distinguish the two groups. Three beneficial bacteria genera (Bifidobacterium, Roseburia, and Subdoligranulum) were significantly enriched in the meditation group with a threshold of 4, according to the LDAs. The functional prediction of differentially enriched intestinal flora showed that the metabolism of tyrosine, propionate, niacin, and nicotinamide in the intestinal micro‐organisms in the meditation group was significantly reduced compared with those in the control group, while the biosynthesis of flavones, flavone alcohols, butosin, and neomycin; flavonoid‐mediated oocyte maturation; cytoskeleton protein pathways; and antigen processing and presentation were significantly enhanced. Conclusions. These results indicate that long‐term vegan meditation plays a positive role in improving the body’s immunity and adjusting endocrine and metabolic levels, enabling the body to be in a state of good health.