The paper explores the effects on soil quality in apple orchard in terms of different soil management systems by comparing the nutrient changes in the soil profiles made during branches covering, natural grass and clean tillage (control). The results show that soil microbial quantity, contents of soil Microbial biomass carbon (MBC), total organic carbon (SOC), easily oxidized organic carbon (ROC) and humic substances (HS) are of vertical distribution characteristics. It means that getting rid of branches covering, natural grass and making clean tillage can improve all the above indices with the decrease of the nutrient contents in the soil profiles. In this process of treating branches covering and natural grass, the number of fungi in the 0-20cm soil layer are increased by 103.61% and 59.18%, bacteria for 94.04% and 65.48%, actinomycetes for 375.27% and 210.75%;MBC contents in the soil are increased by 89.48% and 44.51%, the TOC for 75.48% and 36.75%, ROC for 116.86% and 42%, HS for 114.71% and 88.15%, total GRSP(T-GRSP)for 79.08% and 140.52%; And there is significantly positive correlation between T-GRSP and HS. Thus, branches covering and natural grass in the orchard improve the soil quality, which provides good conditions for the growth of the fruit roots, and this management system is much more scientific and reasonable for orchard soil management.