In the current distributed manufacturing environment, more extensive enterprise cooperation is an effective means for shipbuilding companies to increase the competitiveness. However, considering the project scale and the uneven production capacity between the collaborative enterprises, a key issue for shipbuilding companies is to effectively combine the product-oriented project tasks and the specialized production-oriented plants. Due to information privatization, the decision-making process of project planning and scheduling is distributed and symmetric. Existing project scheduling methods and collaboration mechanisms in the shipbuilding industry are somehow inefficient. The aim of the research is to provide an assistant decision-making method to support effective task dispatching and multi-party cooperation for better utilization of the distributed resources and to help project managers control the shipbuilding process. The article initially establishes an agent-based complex shipbuilding project collaborative planning and symmetric scheduling framework, simulating the distributed collaborative decision-making process and bridging the multi-project planning with the individual project scheduling in much detail, which fills the research gap. A negotiation method based on iterative combination auction (ICA) is further proposed to solve the integration problem of project planning and task scheduling, and an illustrative example is conducted to demonstrate the effectiveness and rationality of the methods. Finally, an application case using a prototype system on shipbuilding projects collaborative planning and scheduling will be reported as a result.