The invention discloses a flexible anti-fatigue structure for a ship body vehicle deck. The flexible anti-fatigue structure for the ship body vehicle deck comprises a longitudinal deck beam, a ship body, a cabin wall reinforcing frame and a deck frame structure, wherein a plurality of inserting gears are arranged on the ship body; the deck frame structure is formed by flexibly hinging a half-gear reinforcing frame and the inserting gears of the ship body; the adjacent deck beams/the half-gear reinforcing frames are respectively arranged in a longitudinal direction/a transverse direction in a staggered manner to form double staggered structure. Without increasing construction difficulty and cost and affecting the normal working of ship roll-on and roll-off equipment, the fatigue strengths at the connected parts of the deck beams and ramps can be furthest enhanced, the safety of the structure can be guaranteed, and the maintenance cost of the destroyed structure can also be reduced.