This study attempted to monitor the development of microbial communities and reveal the correlation between the soil microbial community and soil nutrient factors over different years following the replanting of peach trees.  The replanted soil (RS) and nonreplanted soil (NRS) were collected from peach orchards with different growth years (1, 3, 5, 7, 9, 11, and 13 years) in the same region.  The soil bacterial and fungal community diversities were analyzed by high-throughput sequencing technology.  Redundancy analysis (RDA) was used to show the correlation between the soil microbial community and environmental variables.  The alpha diversities of the bacterial and fungal communities indicated that RS contained a higher abundance of bacterial and fungal operational taxonomic units (OTUs) than NRS.  NMDS and ANOSIM analyses showed that the soil bacterial and fungal communities were significantly (P<0.01) affected by planting years, and that the main changes occurred in the first and ninth planting years.  The presence of the bacterial orders Sphingobacteriales, Burkholderiales and Actinomycetales changed significantly after replanting.  Some bacteria associated with bioremediation, such as Burkholderiales and Intrasporangiaceae, and some harmful pathogens, such as Penicillium and Ophiostomatales, significantly increased after replanting (LDA score>3.0).  In addition, the soil nutrient contents were lower in RS than in NRS in the early stage (1–5 years), and the RDA showed that bacterial and fungal phyla are closely associated with environmental variables, including the potential of hydrogen (pH), ammonium nitrogen (AN), available phosphorus (AP) and available potassium (AK).  These results lead to a deeper understanding of the microbial responses to replanting in peach orchards.