As the primary producers in lakes and reservoirs, phytoplankton assemblages act promptly to environmental changes. They are the most important biological indicators for evaluating the status of aquatic ecosystems. It is a challenging task in freshwater ecology to reveal the driving mechanism of phytoplankton succession and their structural responses to environmental changes through the information within their assemblages. Ecologists ascribe phytoplankton species sharing identical or similar life style and living strategy into a basic unit-"functional group" in the response analysis to environmental change. As functional groups could accurately reflect the changes of aquatic environments, the functional grouping methods have been widely applied in many aspects of freshwater phytoplankton ecology. The classification of functional groups has also been improved and supplemented in the recent applications. The most popular functional classification systems are the FG (Functional Groups), MFG (Morpho-Functional Groups), MBFG (Morphology-Based Functional Groups) and PFT (Plant Functional Types). These classification methods have been used recently to analyse the relationship between phytoplankton assemblages and their aquatic environmental variables in China. As there existing fundamental difference between these classification methods, the users usually face difficulties in ascribing clearly every phytoplankton species into the right functional groups. The paper reviewed the features of each classification method and its application to improve the application in China.