In order to clarify the impact of branch covering on soil microbiology in pear orchards and to analyze the vertical change characteristics of soil and microorganisms under continuous years of branch covering，the characteristics of physicochemical properties of branch covered(5 years)soil at five different depths of 0-10，10-20，20-30，30-40，and 40-50 cm were investigated and three generations of full-length amplicon sequencing of bacteria and fungi were analysed using the PacBio platform. The results were as follows:(1)Branch mulching significantly enhanced soil fertility，particularly in the shallow layer，where organic matter and alkali-hydrolyzable nitrogen content increased by approximately 50%. This effect diminished with increasing soil depth；(2)Branch covering improved microbial diversity，intelligently regulated microbial abundance，and improved microbial uniformity；(3)Soil microorganisms at the phylum level were mainly composed of Proteobacteria and Ascomycota，accounting for over 34.00%，and at the genus level mainly composed of Chujaibacter(<11.00%)and Pseudeurotium(<45.00%)，and at the species level mainly composed of Paraburkholderia_sartisoli(<5.00%)and Pseudeurotium_sp(<45.00%)，and the relative abundance of each soil layer under branch cover was lower than that of the control，branch covering had a greater effect on fungal abundance than bacterial；(4)Bacterial function was predominantly Metabolish(>46.00%)and fungal function was predominantly Saprotroph(29.00%-61.00%)，both with highly significant relationships to major phyla. Branch covering had a lesser effect on bacterial function and a greater effect on fungal function. In conclusion，branch covering，as a new way of soil management in rows，had an important role in solving waste branches，improving soil nutrients and improving soil microbial community，which could provide reference for subsequent research and application of branch mulching.