The invention provides a ship structure and an operating method thereof. The ship structure comprises a main ship and a movable rear ship which is up-down movably pivoted at the rear part of the main ship opposite to the main ship through a hinge linking device; the inner part of the movable rear ship is provided with an engine and a thruster extending out of the outer part of the ship from a thruster shaft, and the tail part of the movable rear ship can be lifted through a lifting device to adjust the height of an off-water line at the rear end of the rear ship and the pivoting angle relative to the main ship. The bottom of the ship is provided with at least one cushion concave part, generally a plurality of cushion concave parts, and pressurized air is filled in the cushion concave parts to reduce the sticky resistance of the bottom of the ship and water. When the ship suffers from storm to generate longitudinal shake to enable the tail part of the ship to raise, the rear ship falls by using a hinge shaft as a center through weight per se for avoiding the idling of the thruster leaving the water level; when the head part of the ship raises, the rear ship raises to maintain normal draught height through the buoyancy of water. The whole ship automatically adjusts the draught area of the thruster and maintains the best navigation state, thereby greatly saving fuel.