In order to realize green manufacturing in the production process of semi-combined marine crankshaft structural parts, good job scheduling and reasonable workshop layout are the key. In traditional method, flexible job shop scheduling problem (FJSP) and the multi-row workshop layout problem (MRWLP) are regarded as separate tasks. However, the separate optimization method ignores the interaction between FJSP and MRWLP. Because the process sequencing of FJSP affects the layout results of processing machines, while the layout scheme of MRWLP affects the scheduling completion time through the transportation between processes. Therefore, it is very important to establish an integrated mathematical model for optimization of both layout and scheduling simultaneously to explore the common influence of the two resource constraints on scheduling results. At the same time, the transportation task is also a manufacturing process that cannot be ignored, which affects the completion time and energy consumption of the workshop, especially the heavy industrial manufacturing workshop with crane as transportation equipment. According to the established model, a five-segment coding including transportation information, layout information and processing information is designed, and two heuristic selection strategies are integrated into non-dominated sorting genetic algorithm II (NSGA-II) to optimize the iterative results twice. Finally, the effectiveness of the integrated mathematical model is verified by an example, which provides guidance for green manufacturing in the shipbuilding industry.