The invention discloses an automatic container wharf loading and unloading system and method. The automatic container wharf loading and unloading system comprises a storage yard, a wharf, a longitudinal road, a shore bridge, storage yard loading and unloading equipment and an in-port truck, wherein the storage yard is divided into automatic closed area storage yards and non-automatic area storageyards, the longitudinal road is divided into automatic closed area lanes and non-automatic area lanes, and the automatic closed area storage yards and the non-automatic area storage yards are arrangedat intervals; isolation fences are arranged between the automatic closed area lanes and the non-automatic area lanes; and special operation channels are arranged on the front edge of the wharf and the two sides of the land area, and isolation enclosures are arranged on the two sides of the special operation channels. Compared with the prior art, only the roads in the port area of a traditional container wharf needs to be isolated again through the fences, meanwhile, the storage yard loading and unloading equipment is automatically transformed and does not need to be replaced, large-scale transformation on civil facilities is not needed, the automatic transformation cost of the traditional container wharf is reduced, the transformation time is shortened, and the operation can be realized while transformation is carried out.