The gut microbiota plays a crucial role in nutrient absorption, health maintenance and protecting the host against pathogen invasion. Studies have shown that the microbial composition and diversity of gut microbiota during early life can influence later growth and development. While specific pathogen-free (SPF) experimental animals are considered standard in biomedical, veterinary, and production research fields, little is known about the composition and diversity of the gut microbiota during the early developmental stages of these birds. Therefore, the present study aimed to explore the structure and changes of the gut microbiota during the early life of SPF chickens. Faecal DNA was sampled from randomly selected chickens, followed by high-throughput sequencing of the V3-V4 region of the 16S rRNA gene, at 11, 13, 15, and 17 days of age, designated as experimental groups D11, D13, D15, and D17. The sequencing results indicated that day 17 of life may be a turning point for gut microbiota colonisation, exhibiting a notable 51.98% increase in the number of operational taxonomic units compared to 15 days old birds. Analysis of faecal bacterial community compositions across the four age groups of SPF chickens showed dominance of Firmicutes, Proteobacteria, and Bacteroidetes in groups D11, D13, and D15, while Firmicutes, Proteobacteria, and Cyanobacteria were dominant in group D17. Additionally, group D17 had the highest number of bacterial genera and greatest diversity among the four groups tested. This study systematically elucidated the structure and dynamics of the gut microbiota during early life of chickens and provided a benchmark for future research on chicken gut microbiota.