As an advanced stage and manifestation of facility agriculture, plant factories facilitate highly controllable and uninterrupted industrial production of crops throughout the year. With advancements and applications in plant synthetic biology, systematic design and modification of plant genes, metabolic pathways, and physiological functions through engineering approaches are now being integrated with plant factories in various areas, including the production of plant secondary metabolites, molecular agricultural products, enhancing resource utilization efficiency, and the creation of carbon sink plants. This integration is transitioning from the laboratory to industrialization. The high-value sustainable development of plant factories and the collaborative innovation between industry and technology was delved. It elaborated on the combined applications of plant synthetic biology and plant factory production technology in fields such as bio-manufacturing, drug development, endangered plant conservation, and future space stations. Furthermore, it explored the future directions and challenges of this integration, offering novel solutions to expand the boundaries of agricultural production possibilities, achieve efficient supply of high-value agricultural products, and foster diversified development of agricultural resources.