The present invention relates to an apparatus for controlling the environment of a greenhouse having a multi-shell structure, a method and a system thereof, and a system for controlling the environment of a greenhouse according to the present invention comprises a first greenhouse forming layer using a hard or soft transparent material; At least one second greenhouse forming layer using a hard or soft transparent material and being entirely surrounded by the first greenhouse forming layer with a predetermined spacing from the first greenhouse forming layer; A plurality of first top side windows provided on a roof and side walls of the first greenhouse forming layer; A plurality of second side windows provided on the roof and sidewalls of the second greenhouse forming layer: an environmental sensor for measuring data on the inside or outside environment of the greenhouse; A plurality of first and second side windows formed by opening and closing the first and second side windows in consideration of the size and position of the first and second side windows and the air flow between the first and second side windows; A ventilation mode part for calculating a ventilation amount for the ventilation path and setting a plurality of ventilation modes; And controlling the opening and closing of the first top-side window and the second top-side window so as to operate in any one of the plurality of ventilation modes according to the required ventilation amount, based on the measured result of the environmental sensor unit And a greenhouse control unit. Accordingly, the ventilation path can be lengthened according to the opening / closing combination of the plurality of top-end windows, thereby reducing the direct influence of outside air and controlling the greenhouse environment so that the temperature deviation is not large.본 발명은 다중 외피 구조를 갖는 온실의 환경제어장치, 그 방법 및 시스템에 관한 것으로, 본 발명에 따른 온실의 환경제어시스템은 경질 또는 연질의 투명 재료를 사용하는 제1온실형성층; 경질 또는 연질의 투명 재료를 사용하고, 상기 제1온실형성층과 소정 간격 이격된 채 상