The invention discloses an indoor intensive aquaculture system and belongs to the field of mariculture. The indoor intensive aquaculture system comprises a reservoir, a preheating pond, a deep well, a fan chamber and an aquaculture greenhouse; natural seawater in the reservoir enters the preheating pond, is heated by terrestrial heat of well water in the deep well, and enters the aquaculture greenhouse. The system has the characteristics of simulation of natural ecological environment, easiness in cleaning dirt and energy conservation and solves the problems that dirt is not easy to clean, the growth rate of cultured creatures is low, the aquaculture density is low and the cultured creatures are easily attacked by a disease in the conventional industrial aquaculture process; moreover, the temperature of the aquaculture system is improved by using natural energy, and the aquaculture cost is reduced.