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The problem of heterogeneous data, caused by the differences of marine data acquisition equipments, information processing platforms, data storage formats, makes the data integration, exchange and share difficult. Nowadays, the problem of data semantics in heterogeneous data integration is even more severe. Aim at solving this problem, we introduce an ontology-based automatic ETL (Extract, Transform and Load) method. This method can be achieved automatically as follows:Firstly, extracting the data structures and data semantics from source data sets, secondly, achieving the match from the source data sets to target database, thirdly consider the data structures and semantics aspects based on the target database, and finally, load the data from target database. Case study shows this method improve the quality of the data and the efficiency of data integration. This method solves the problems leaded by heterogeneous data, in particular, the semantic heterogeneity.