The traditional functional organizational structure of the ship repair plant cannot meet the needs of modern production in the process of support with the increasing complexity of ship equipment. In view of the above problems, different management organizational structures are analyzed and compared to propose a hybrid organizational structure based on strong matrix organizational structure, which effectively improves the horizontal communication efficiency between cross departments. At the same time, a compensation model of “salary + incentive + reward” is proposed, which increases the enthusiasm of employees. Finally, the application of the hybrid organizational structure in modern shipyards in the first level repair process of a ship in a shipyard are analyzed through a survey questionnaire. It can provide ideas for the organization and management of modern shipyards.