In order to study the effect of planting years on the rhizosphere soil microbial activity and function of healthy Sanqi ginseng, rhizosphere soils of 1- and 2-year-old healthy Sanqi ginseng were collected, and fluorescein diacetate hydrolysis method, real-time quantitative PCR and Biolog assay were employed to analyze soil microbial activity, nitrogen functional gene abundances, metabolic activity and functional diversity. Results show that Sanqi ginseng planting significantly enhances soil microbial activity as compared to uncultivated soil, and soil microbial activity is continuously increased with the growth of Sanqi ginseng. Similarly, the abundance of nitrogen-related functional genes (nifH and bacteria amoA) is also increased in response to Sanqi ginseng cultivation and planting years, indicating that nitrogen availability might be enhanced by the rhizosphere microbes and is for the nutrient requirements of Sanqi ginseng. Moreover, rhizosphere soil metabolic activity and functional diversity indices are also improved by Sanqi ginseng planting, and they are increased along with Sanqi ginseng growth. In addition, Sanqi ginseng planting years alters carbon source utilization pattern of rhizosphere microbes. Interestingly, the utilization efficiencies of carbohydrates, carboxylic acids, amino acids, amines, and polymers by rhizosphere microbes are increased with Sanqi ginseng planting years, whereas the utilization efficiency of phenolic acids is not differed significantly with the growth of Sanqi ginseng. Therefore, lower degradation activity of rhizosphere phenolic acids is an important reason for its accumulation and thereby drives the imbalance of rhizosphere microbiomes as well as the formation of continuous cropping obstacles. These results can not only provide data support for understanding rhizosphere microbial activity and metabolic function of healthy Sanqi ginseng, but also provide theoretical basis for the interpretation of formation mechanism of continuous cropping obstacles of Sanqi ginseng.