The invention provides an intelligent joint robot stacking system and a control system thereof. The intelligent joint robot stacking system comprises a front-section conveyor, a reshaping conveyor, a fetching position raceway, a stacking position raceway machine, a stacking rear heavy tray raceway machine, a tray sending chain machine positioned on a tray library, a corner raceway machine on a tray library, an intelligent joint robot stacking machine and a device control system, wherein the device control system adopts a PLC (Programmable Logic Controller) control technology; equipment, such as an intelligent stacking machine, the intelligent tray transmitter, a conveying belt machine, a power raceway and the like, is organically combined with various detection elements and pneumatic elements; and under the control of a main control unit, one joint robot stacking machine is adopted to distinguish and automatically stack different products. According to the intelligent joint robot stacking system and the control system thereof, manpower can be saved, heavy manual work is liberated, and various possible errors which possibly appear during manual operation are avoided. The production efficiency is improved, the system can stably and reliably work, the equipment use ratio is improved, the equipment investment is saved, and the energy consumption is lowered.