The invention discloses a seawater greenhouse. The length direction of the seawater greenhouse is along the east-west direction, and the north wall is of a brick structure; a double-layer plastic film is arranged at the top of the greenhouse; a heat insulation quilt is laid outside the double-layer plastic film; a stichopus japonicus pool is arranged in the greenhouse; part of the stichopus japonicus pool is located underground, and the underground part accounts for 2/3 of the whole height of the stichopus japonicus pool; meshed reef or stone reef is paved at the bottom of the stichopus japonicus pool; furthermore, the paving area of the meshed reef or stone reef accounts for 40 to 60 percent of the total area of the bottom of the stichopus japonicus pool; a water feeding and drainage pipeline is further arranged on the stichopus japonicus pool; a sea urchin pool is further arranged in the greenhouse; a distance from the bottom of the sea urchin pool to the ground is 1 m; a water feeding and drainage pipeline is further arranged on the sea urchin pool; meanwhile, a submersible pump is further arranged in the stichopus japonicus pool; the tail end of a water drainage pipe of the submersible pump is located in the sea urchin pool; a water drainage pipe which communicates with the stichopus japonicus pool and is provided with a valve is arranged on the sea urchin pool; and a sidewalk distributed along the length direction of the greenhouse is also arranged in the greenhouse. Moreover, the invention further discloses a method for comprehensive ecological aquaculture by using the greenhouse.