The initial bacteria in a newborn's gastrointestinal tract come from the mother's birth canal, the environment, and breast milk. Gut microbiota is established earlier in infants delivered naturally than by cesarean section (C-section). Gut microbial diversity increases further as infants reach weaning, with the addition of complementary foods and increased food diversity. Upon reaching adulthood, the composition of the microbiota is relatively stable, with , and as the main microbiota. The development of gut microbiota in children, as well as the potential disruption of newborn gut microbiota development by antibiotics, necessitates the development of new nutritional foods to address the challenges of gut microbiota and nutrition in children. Specific probiotic strains may prevent acute gastroenteritis, antibiotic diarrhea, infantile colic, and necrotising enterocolitis (NEC). Microecological preparations such as probiotics are a group of live microorganisms that provide health benefits to the host when given in sufficient quantities, and are mainly categorized into live bacteria in bulk, tablets and capsules. Probiotics are currently widely used in the treatment of gastrointestinal related diseases, and have achieved certain results in clinical practice as a supplement to conventional therapies. However, there are still not many types of microecological preparations that have isolated strains. Finding probiotics that target a particular disease and isolating them is a difficult part of the development of microecological preparations for clinical applications. At present, in the clinical cohort study of children using probiotic preparations, microecological preparations either show their ability to prevent diseases or are mostly used as auxiliary means of traditional therapy. Although there are fewer clinical cohort studies with microecological preparations as the primary treatment, their clinical application will be increasingly promising. This review aims to systematically summarize the formation patterns of gut microbiota in children, analyze the mechanisms of action of microecological regulators, and evaluate their clinical applications in pediatric diseases, thereby providing insights for addressing gut microbiota-related challenges.