In order to reveal the changes of soil micro-ecological environment of continuous cropping watermelon in greenhouse，high-throughput sequencing was used to sequence and analyze the soil samples of continuous cropping group(soil of continuous cropping watermelon in greenhouse for ten years)and control group(soil of open-air cropping watermelon soil with the same texture as the soil around continuous cropping watermelon in greenhouse for ten years). The community structure of soil bacteria and fungi between two groups were compared，and the soil physicochemical properties and enzyme activity were determine. The results showed that soil pH，ammonium nitrogen，available potassium，microbial biomass carbon and soil enzyme activity in continuous cropping group were significantly lower than those in control group，while nitrate nitrogen and available phosphorus were significantly higher than those in control group. The ACE index and Chao1 index of bacteria in soil of continuous cropping group were significantly higher than those of control group. The ACE index，Chao1 index，Simpson index and Shannon index of fungi in soil of continuous cropping group were lower than those of control group. The dominant species composition of soil bacteria and fungi changed. In bacteria，compared to the control，the relative abundance of Proteobacteria，Gemmatimonadetes，Chloroflexi and Nitrospirae in the continuous cropping group increased by 9.80%，20.83%，21.76% and 27.12%，respectively(P<0.05)，Acidobacteria and Verrucomicrobia reduced by 21.7% and 26.27%，respectively(P<0.05). In fungi，the relative abundance of Ascomycota increased by 10.96%(P<0.05)，and the relative abundance of Basidiomycota and Rozellomycota decreased by 13.42% and 93.77%(P<0.05)，respectively. Correlation analysis showed that the dominant bacteria except Latescibacteria and Rokubacteria were not significantly correlated with all soil environmental factors，and other dominant bacteria were closely related to the measured soil environmental factors(except organic matter). Soil pH，ammonium nitrogen，available phosphorus and available potassium were the main factors affecting soil microbial community. Basidiomycetes and Chloroflexi could indicate soil microbial biomass. The change of microbial community structure had a great influence on enzyme activity. In summary，the soil physical and chemical properties，enzyme activity，bacterial and fungal community structure changed significantly after 10 years of continuous cropping of watermelon in greenhouse. Continuous cropping obstacle of watermelon in greenhouse was the result of many factors.