The problem of short stature in children has received increasing attention in recent years, and the factors affecting growth and development in children are complex. The gut microbiota is closely related to the human neuroendocrine system, immune metabolism, growth and development. Previous studies have shown that gut microbiota and their metabolites can regulate host growth. In this paper, the mechanism and prospects of the effects of gut microbiota and their main metabolites, short-chain fatty acids, on growth hormone/insulin-like growth factor-1 axis, thyroid gland and sex hormones were reviewed from the endocrine point of view, in order to provide new ideas for improving short stature in children in the future. [ABSTRACT FROM AUTHOR]