The effects of different microbial fertilizers and chemical fertilizers on the growth of lemon seedlings and the improvement of the soil were explored to provide reliable basis for scientific fertilization of lemon seedlings.“Yunning No. 1” lemon seedlings were taken as test materials，the effects of different microbial fertilizer and chemical fertilizer combined application on the plant growth and soil physicochemical properties were studied，in order to obtain the optimal combination of microbial fertilizer and chemical fertilizer.The results showed that in the treatments of four bacterial agents combined with chemical fertilizers of Arbuscular mycorrhizae，Penicillium baili，Bacillus subtilis and Composite strains，from the comprehensive perspective of plant growth and soil nutrient status，the best treatment was the application of 83.3 mL/plant Penicillium baili combined with 20 g/plant lemon fertilizer，which significantly increased the contents of organic matter，available potassium，alkali hydrolyzable nitrogen，medium and trace elements in soil and the chlorophyll content of the plant leaves by 142.88%，305.63%，72.22%，32.66%，and 43.23%，respectively，compared with the control (CK，single application of chemical fertilizer)，and the soil pH value kept in the suitable range for lemon to growth.The plant showed that the trunk was thickened，the crown width was uniform，and the proportion of vegetative branch and fruiting branch was coordinated.The leaf area and leaf fresh weight increased significantly，which were 211.11% and 20.68% higher than that of CK.On the whole，the effect of the combined application of four kinds of microbial fertilizer and chemical fertilizer showed as follows:Penicillium baili> Arbuscular mycorrhizal fungi > Complex strains > Bacillus subtilis > CK.The combined application of four kinds of microbial fertilizer and chemical fertilizer could promote the growth of lemon seedlings，improve the soil nutrient status，and increase the contents of organic matter，nitrogen，phosphorus，potassium and mineral elements in the soil，and the combined application of penicillium baili-chemical fertilizer had the best effect.