This invention provides a transgenic plant factory (1) comprising a closed cultivation area (2) being kept at negative pressure and equipped with hydroponic system (4) for cultivating transgenic plants (P) and air-conditioner (5) with exhaust air-filter, an inactivation area (20) located next to said cultivation area (2) via air-locked passage (22) and being kept at negative pressure less strong than that at the cultivation area (2) and equipped with inactivation system (21) to prevent post-harvest transgenic plants (P) from sprouting, growing, proliferating or hybridizing, a manufacturing area (30) located next to said inactivation area (20) via air-locked passage (38) and being kept at positive pressure and being equipped with system (42, 43) for processing and/or preparing the post-harvest plants (P) into foodstuffs and/or pharmaceuticals, a sterilizer (60) for sterilizing the drainage from cultivation area (2), and air-locked workers' gateways (10, 14, 39, 35) provided to the cultivation area (2) and the manufacturing area (30) respectively.