The invention belongs to the field of mechanical equipment and particularly relates to an automatic pharmaceutical glass packaging and integrating system. The automatic pharmaceutical glass packaging and integrating system is characterized by comprising a transfer robot, a pallet conveying line, a backing plate conveying line, a cover plate conveying line, a capturing line, a heavy tray conveying line and a stacking area, wherein the pallet conveying line, the backing plate conveying line, the cover plate conveying line, the capturing line, the heavy tray conveying line and the stacking area are distributed around the transfer robot. The pallet conveying line is connected with a pallet supply machine, the capturing line is connected with a hot pack conveying line, a full-automatic rotary packing machine is arranged on the heavy tray conveying line, and a composite manipulator is mounted on the mechanical arm of the transfer robot and is connected with a PLC (programmable logic controller) system. The integral automatic pharmaceutical glass packaging and integrating system can be monitored in all around by the PLC system during running. Hot packs can be conveyed and stacked automatically, backing plates can be added automatically, cover plates can be automatically captured and placed, and trays can be automatically packed. The automatic pharmaceutical glass packaging and integrating system is convenient and quick to operate, labor intensity is reduced, extra equipment investment is reduced and economic and practical purposes are achieved. The conveying lines distributed within a circumference taking the gravity center of the transfer robot as a circle center are reasonable and compact in arrangement.