Abstract: Effects of nitrogen (N), organic fertilizer and their combination on the rhizosphere microorganisms and root growth of M. hupenensis Rehd. seedlings (2 years old) were investigated. The results showed that fertilizer application increased the numbers of rhizosphere microorganisms with the exception of nitrogen-fixing bacteria. Fertilizer N at the concentration of 500 mg/kg decreased the number of bacteria, actinomycetes and cellulolytic microbe, which were reversed by applying organic fertilizer at the concentrations of either 3% or 6% (the percentage of dry soil weight). The combination of 3% organ fertilizer and 200 mg/kg N had the best effect on alleviating the unfavorable effect of higher concentration of N (500 mg/kg). The number of bacteria, fungi, ammonifier and nitrobacteria were positively correlated with the biomass of growing roots and absorbing roots, while the number of nitrogen-fixing bacteria was negatively correlated with absorbing root biomass. Correlation between number of cellulolytic microbe and root biomass was not detected. Only numbers of bacteria and cellulolytic microbe were positively correlated with root respiration rate of the M. hupenensis Rehd.seedlings.