Classification is the key to understanding changes in aquatic habitats. Most of the existing classifications were proposed for different purposes such as specific research and management needs and there are no commonly applied criteria for the classification, thus their operability and comparability are limited. Therefore, the purpose of this study was to propose a multifunctional classification system of aquatic habitats that embraces the advantages of remote sensing data based on the system theory, so that the classification can be practical and comparable. Additionally, this study provided the interpreting marks of different types of aquatic habitats for Landsat remote sensing data. Based on the interpreting marks, this study obtained the spatial distribution and areal ratio of different types of aquatic habitat in China by using the Landsat remote sensing data in 2015. The multifunctional classification of aquatic habitats for remote sensing data is the foundation for understanding changes in aquatic habitats.