Tongue inspection is a unique and important method of diagnosis in traditional Chinese medicine (TCM). It is a diagnostic approach which involves observing the changes in the tongue proper and tongue coating in order to understand the physiological functions and pathological changes of the body. However, the biological basis of TCM tongue diagnosis remains to be poorly understood and lacks systematic investigation at the molecular level. In this study, we evaluated the effects of tongue coating microbiome on changes in the tongue texture and coating in patients with post-menopausal osteoporosis (PMO) of Gan‑shen deficiency syndrome type. Our aim was to delineate the mechanisms of tongue coating microbiome-induced changes in the tongue texture and coating by investigating the histomorphological changes and performing a bacterial analysis of the tongue coating. We found that the number of intermediate cells in the red tongue with a thin coating was higher, while the number of superficial cells in the red tongue with a thin coating was lower. The maturation value (MV) of tongue exfoliated cells in the red tongue with a thin coating decreased, compared with that in the pale red tongue with a thin white coating. Furthermore, the total bacterial count, oral streptococcus, Gram‑positive (G+) and Gram‑negative (G-) anaerobic bacteria in the red tongue with a thin coating was significantly decreased compared with the pale red tongue with a thin white coating. The results of ultrastructural examination demonstrated that the number of epithelial cells and bacteria in the red tongue with a thin coating decreased compared with that in the pale red tongue with a thin white coating. These observations indicate that the tongue coating microbiome may be an important factor contributing to changes in the tongue in patients with PMO of Gan‑shen deficiency syndrome type.