Spatial indexing technology is widely used in Geographic Information Systems (GIS) and spatial databases. As a data retrieval technology, spatial indexing is becoming increasingly important in the big-data age. The purpose of this study is to propose a unified indexing strategy for the mixed data of a future marine GIS. First, data organisation of the system is described. Second, the display condition of each type of data is introduced. These conditions are the basis for the construction of a unified indexing structure. Third, a unified indexing structure for mixed data is presented. The construction process and the search method of the indexing structure are described. Finally, we implement the indexing strategy in our system “Automotive Intelligent Chart Three-dimensional Electronic Chart Display and Information Systems” (AIC 3D ECDIS). Our strategy can provide fast and integrated data retrieval. The spatial indexing strategy we propose breaks through the limitation of data types in our system. It can also be applied in other GIS systems. With the advent of the big-data age, mixed data indexing will become more and more important.