Abstract: In order to understand the changes of microbial community structure after the improvement of greenhouse pepper continuous cropping soil in Fujian Province, the soil conditioner of oyster calcium was applied to the continuous cropping soil of greenhouse pepper at 900 kg·hm^-2 to improve the soil, and then the pepper was planted. At the end of planting, the planting soil in which the greenhouse pepper could grow healthily (JK), the soil with continuous cropping obstacle (LZ) and the improved (GL) planting soil were collected for the detection and analysis of microbial diversity. The results showed that the bacterial richness and diversity of JK soil were the highest, the fungal richness and diversity of LZ soil were the highest, and the bacterial and fungal richness and diversity of GL soil were in the middle. The further analysis showed that the number and species of bacteria in GL soil were closer to that in JK soil, while the number and species of fungi in GL soil were closer to that in LZ soil. The OTU clustering results of the top 10 bacterial richness showed that three samples in each group of JK soil, GL soil and LZ soil could be clustered into an independent cluster unit, and the phylogenetic relationship between GL soil and JK soil was closer. The dominant bacteria in the three kinds of soil were different, and the proportion of Basidiomycetes in LZ soil was much higher than that in JK soil and GL soil. It indicated that the addition of soil conditioner could change the microbial community composition of continuous cropping soil and change towards the healthy soil.