The invention discloses a ship bottom safety inspection method, and belongs to the technical field of safety inspection. According to the method, ship bottom safety inspection work areas of a ship bottom scanning area, a ship bottom suspicious target identification area and a control command center are arranged firstly; a ship bottom underwater safety inspection device performs acoustic scanning on a ship which passes above the ship bottom underwater safety inspection device and uploads data to the control command center; the control command center forms a three-dimensional image of a ship bottom underwater part and interprets three-dimensional image of the ship bottom underwater part, and the control command center releases the ship if the control command center does not find ship bottom suspicious objects like attachments and towing objects, or the control command center notifies to perform further inspection; a ship bottom target identification device discriminates the suspicious objects via an acoustic scanning mode or an optical scanning mode, uploads the identification work process and the result and performs corresponding processing; and the control command center monitors the process of sailing into the suspicious target identification area of the ship and the identification work process and records the result. According to the method, the ship bottom safety inspection effect can be ensured and safety inspection efficiency can also be considered.