The invention discloses a full-automatic factory pond multi-layer classified cultivation technology. The pond single-layered polyculture is transformed into the multi-layered classified single-culture, so that independent perfect nests with different levels, different temperatures, different amount of dissolved oxygen, separated bait and excrement, and comfortable environments are respectively provided for cultivated targets of different specifications and different varieties, layered and classified independent cultivation environments with appropriate conditions are respectively provided for phytoplankton, zooplankton, fishes, shrimps, crabs, ginseng and shellfish; the illumination, temperature, dissolved oxygen, nutrient salt, carbon dioxide, pH value and transparency of various layers can be adjusted and controlled at any time, so that an optimal growth environment can be provided for cultivated targets; the functions of running water cultivation, microalgae culture, zooplankton culture, fish culture, shrimp and crab cultivation, shellfish bottom sowing culture, net cage cultivation, autologous water circulation, autologous fertilizer circulation and the like are integrated into a whole; therefore, a modern high-yield, efficient, low-carbon, low-consumption, energy-saving, environment-friendly, water-saving, power-saving, ecological, organic, healthy, one-click managed full-automatic factory pond multi-layered classified cultivation comprehensive management and control system can be realized.