Product footprint management strategies for long-process manufacturing industries generally lack systematic analysis of the interactions between economic, emission, and energy footprints, leading to missed energy conservation and emission reduction opportunities. Accordingly, this paper develops a product economic-environmental-energy footprint coupling assessment and collaborative optimization framework, enabling more precise quantitative analysis and significantly reducing product carbon footprint. Specifically, an integrated model based on Life Cycle Cost (LCC) analysis, Life Cycle Assessment (LCA), and Multi-Regional Input-Output (MRIO) methods is designed to track the costs, energy consumption, and emissions accurately. Given that “end-to-end” footprint assessment methods generally failing to distinguish the sources of high costs, emissions, and energy consumption within the production process, a sub-process-based footprint coupling assessment method is introduced to systematically measure each product’s economic, environmental, and energy impacts. Furthermore, a graph-based multi-objective optimization framework for low-carbon and energy-efficient production layout is established to fully explore the potential for energy conservation, emission reduction, and cost savings. A case study applying the proposed model and methodology to a real-world refinery production site demonstrates that concentrated carbon conversion, allocation, and secondary release are the primary causes of high emissions. After layout optimization, diesel oil’s energy and emission footprints decreased by 71.4% and 73.9%, respectively, showing substantial energy conservation and emission reduction potential. The constructed low-carbon and energy-efficient production layout optimization framework significantly reduces the comprehensive footprint of products and contributes to the green transformation of the refineries.