In order to effectively meet the new requirements raised by the international shipbuilding convention and specification for shipbuilding enterprises, and to quickly improve enterprise innovation capability, this article analyzes the modern shipbuilding characteristics and compares them with the lean production methodology. In China, the shipbuilding enterprise development is guided by the Shipbuilding Industry Standard Conditions assessment rules from the Ministry of Industrial and Information Technology of China. This article proposes establishing an efficient merchant shipbuilding system based on the lean production methodology and the construction technology capability indices in the Shipbuilding Industry Standard Conditions. This article focuses more on the hull construction and merchant ship production processes, instead of the entire engineering, procurement, and construction shipbuilding management. It elaborates key system technologies including value stream analysis, efficient shipbuilding production design, efficient shipbuilding project management, efficient shipbuilding precision management, and efficient full factory management. The efficient shipbuilding system has been implemented in a Chinese merchant shipbuilding enterprise to significantly improve productivity and reduce shipbuilding cycle time.