This study adopts a mathematical modelling method based on geographic information system (GIS) to conduct a comprehensive evaluation of the impact of the construction of the data centre in the sea on the marine environment. Firstly, seven key water quality parameters are selected as evaluation criteria from the actual sea pollution condition and the evaluation of the national marine bulletin, and then, through the fuzzy comprehensive evaluation model and the hierarchical analysis method, the multi-source data are integrated, and the unique advantages of the GIS technology in the expression of spatial information, the construction of spatial models, and the calculation of the fuzzy comprehensive evaluation index of the water quality are utilised to ultimately determine the weights of the various evaluation indexes. From there, the level of seawater quality in the sea surrounding the Sea Central Data Centre is judged. The research results show that the construction of the data centre in the sea has a certain impact on the water quality of the surrounding sea area, but the impact can be reduced to a minimum through rational planning and management.