Aquaculture ecosystem is a special type of industrial ecosystem, which is similar to aquatic ecosystem in natural attributes, and similar to terrestrial agroecosystem in human intervention. Compared with natural aquatic ecosystems, aquaculture ecosystems have four characteristics: First, the energy and material input of the system is not entirely dependent on solar radiation, precipitation, runoff, etc., but partly controlled by human beings; Second, in order to maximize the production of target organisms (farmed animals), the biodiversity of the system has been artificially reduced; Third, biological communities in the system are not naturally formed, and the dominant organisms are usually artificially stocked; Moreover, some aquaculture systems may exert negative impacts on the adjacent environment when the wastewater from the system is discharged. In this chapter aquaculture production systems are classified based on energy sources, systemic metabolic characteristics, nutrient budget and ecological limiting factors. Ecological characteristics and ecosystem services of aquaculture systems are also introduced.