The invention discloses a photoetching method and device of a roll to roll flexible substrate. By designing an exposure infrared transmission path and an exposure mode, photoetching of the flexible substrate is achieved, and process steps of attaching a traditional flexible substrate onto a glass substrate, final substrate stripping and the like are not needed; and on one hand, the process device cost is saved, and on the other hand, the production yield and the production rate are improved. The fabrication process is simple, the production rate can be effectively improved, and rapid and high-quality etching on the flexible substrate can be achieved on the condition of lower production cost. The device disclosed by the invention mainly comprises an infrared light source, a flexible substrate transfer system and a photoresist coating device. The device is simple in structure, and is convenient to use, maintain and fabricate.