In view of the current excessive application of nitrogen (N) fertilizers to apple trees，the effects of replacing chemical fertilizer N with organic fertilizer N at different chemical and organic proportions on root growth of apple trees and changes of soil microorganisms were studied to identify the best replacement ratio of organic fertilizer N to chemical fertilizer N. Field experiments were conducted in a perennial Red Fuji apple (Malus pumila Mill) orchard with seven treatments:op-timized chemical fertilizer application (Y1)，replacing 20% chemical N fertilizer with conventional organic fertilizer (Y2)，replacing 40% chemical N fertilizer with conventional organic fertilizer (Y3)，replacing 60% chemical N fertilizer with conventional organic fertilizer (Y4)，replacing all chemical N fertilizer with conventional organic fertilizer (Y5)，conven-tional organic fertilizer replacing three times of total N (Y6)，fruit branch organic fertilizer replacing three times of total N (Y7). Dry weight of plant roots，the diversity of carbon source utilization of soil microorganisms and other microbial indi-cators were measured. Concentrated fertilization in ditch can significantly increase root dry weight，root surface area and root configuration，thus increase the ability of root to absorb nutrients and water. The proportion of conventional organic fertilizer replacing nitrogen fertilizer which is most beneficial to root growth is 40%～60%；fruit branch organic fertilizer instead of nitrogen fertilizer can also promote root growth，but the best ratio needs further experimental verification. Local applica-tion of organic fertilizer in 0～30 cm root dense area increased the root dry weight，surface area and volume of soil layer to some extent，but decreased the root length. The suitable ratio of conventional organic fertilizer to replace nitrogen fertilizer is 40%～100%，and fruit branch organic fertilizer is less effective than conventional organic fertilizer. Using BIOLOG method to measure soil microbial diversity in different treatments，it was found that in the complete culture cycle，the change rates of AWCD and the final AWCD values in all treatments except Y4 were lower than those in the Y1(control). Compared with Y1，The richness of soil microbial community decreased，the diversity difference was not significant，and the evenness was improved. The main components of carbon source utilization were alcohols and amino acids. Considering the substitution effect of organic fertilizer on nitrogen fertilizer，the improvement of root growth environment and the promotion of fruit root growth and root activity，replacing chemical N fertilizer with organic fertilizer for more than 40% N has obvious biological effects in improving the growth environment of apple tree roots and promoting growth and vitality of apple tree roots. Considering the slow-release effect of organic fertilizer and the acceptance of apple farmers，40% is the best ratio for the use of conventional organic fertilizer replacing chemical N fertilizer. The best substitution ratio of fruit branch organic fertilizer needs further research and verification.