Microbial diseases are one of the main diseases faced by ancient wooden shipwrecks after salvage. Among them, the growth and metabolism of microorganisms in the water/soil environment where ancient shipwrecks are located may directly damage the shipwrecks or affect the safety of cultural relics by changing the environment. Meanwhile, the change of environmental factors also has a reverse effect on the community structure and metabolic characteristics of microorganisms. Therefore, environmental factors and microbial communities form a dynamic system that affects each other. It is an important direction for the conservation of ancient wooden shipwrecks to study the mechanism of interaction between microorganisms and environmental factors in a systematic and in-depth way, identify and even predict risks in time and adopt scientific and effective prevention and control strategies. In this study, the characteristics of environmental factors, microbial community structure and potential disease-causing microorganisms before and after salvage of the Yangtze River Estuary No.2 shipwreck were studied through environmental monitoring and sequencing technologies. The results show that:1) before and after salvage of the Yangtze River Estuary No.2 shipwreck, the change of water environmental factors was bigger, and the microbial richness and diversity decreased significantly, especially the bacterial richness; 2) the change of sediment environmental factors was smaller, and the richness and diversity of microbial community also changed less. The main microorganisms involved in the degradation of lignin and cellulose in the sediment and water environment were Bacillus, Aspergillus and Cladosporium. In addition, a high proportion of sulfate-reducing bacteria in the sediment need to be considered. This study has initially established a monitoring and assessment system for environmental factors and disease-causing microorganisms of the Yangtze River Estuary No.2 shipwreck, laying a foundation for the subsequent scientific and systematic accumulation of basic data, which could then be used to assess and even predict the environmental microbial risk status of the Yangtze River Estuary No.2 shipwreck through statistical analysis and modeling.