In forests, seedling renewal is influenced by many environmental factors, including climate change, seed size, wildfires, and ecological factors. It is unclear how different growth years of seedlings affect Chinese cork oak (Quercus variabilis) root endophyte communities. In this study, we took a holistic approach, using Illumina sequencing, to study the composition and function of bacterial communities associated with root microorganisms in four Q. variabilis seedlings after 1, 2, and 3 years of growth. The bacterial alpha diversity indexes were highest in the second year and lowest in the third year, and age was the decisive factor for the differences found in the root endophytic bacterial communities. Total phosphorus had the greatest effect on bacterial communities. The abundance of beneficial bacteria Streptomyces (8.69%) and Novosphingobium (4.22%) was highest in the second-year samples, and their abundance decreased by 7.96% and 3.61% in the third year, respectively. Higher levels of plant disease inhibition and metabolism (23.80%) were in the roots of second-year Q. variabilis seedlings. The metabolic abundance of carbohydrate was 3.66% lower in the first year and 3.95% lower in the third year compared to the second year. Our results suggest that the structure and function of bacterial communities changed with increasing growth years.