Human industrialization has caused damage to ecosystems. In this context, researchers have developed several methods to assess the health of various types of ecosystems. In this paper, we evaluated the developmental history and status of ecosystem health (EH) and summarized the concept of EH. We also reviewed ecosystem health assessment (EHA) methods and analyzed the application of EHA methods. EHA methods are generally classified into biological indicator and index system method. The former method is mainly based on the number of dominant species, such as diatom, plankton, and macroinvertebrate. Results indicate that trophic diatom index (TDI), plankton index of biotic integrity (P-IBI), and Ephemeroptera, Plecoptera, and Trichoptera (EPT) are the most commonly used indices. The latter method combines multiple ecosystem metrics and reflects ecosystem processes. The pressure–state–response (PSR) model most commonly uses the index system method. For the application of EHA methods, biological indicator methods are mostly applied in rivers/streams ecosystem, while the index system is primarily involved in urban ecosystems. Therefore, the information presented in this review may be helpful for the modification of EHA methods.