The method of location-based fertilization was used to reduce the amount of fertilizer and apply cow manure in the same protection plot for many times. In the experiment of greenhouse vegetable planting，four different chemical fertilizers，including the control(CK，single compound fertilizer 2250 kg/hm²)，low(L，66.7% CK+organic fertilizer 30000 kg/hm²)，medium(M，33.3% CK+organic fertilizer 45000 kg/hm²)，and high(H，single organic fertilizer 60000 kg/hm²)，were set up to explore their effects on the soil basic fertility，root bacteria，fungi，actinomycetes as well as crop yield and quality.The results showed that with the increase of the proportion of reducing fertilizer and organic fertilizer，the content of total nitrogen and available phosphorus in 0～20 cm soil also showed an increasing trend，and with the increase of the number of planting stubble，the differences among the treatments were more and more big.Compared with the control，the combination of chemical fertilizer and organic fertilizer increased the number of bacteria and actinomycetes in the root soil of crops，and reduced the number of fungi.In terms of yield and quality，the treatment of M was the best，in particular，the fourth crop of Capsicum increased production by 12.37% compared with the control，the content of vitamin C was 33.52% higher than that of the control.