The invention discloses a wafer box automatic positioning mechanism. The wafer box automatic positioning mechanism comprises a rectangular wafer box tray; a reference block is fixedly mounted on one side of the wafer box tray; linear guide rails are respectively arranged on other three sides of the wafer box tray; adjusting blocks are mounted on the linear guide rails; adjusting block connecting pieces are arranged at the top ends of the adjusting blocks, and are connected with driving motors; and the driving motors are connected with drives. The invention further discloses a wafer box carrier vehicle; the wafer box carrier vehicle comprises an automatic guide carrier vehicle; the automatic guide carrier vehicle comprises a vehicle body and a frame positioned on the vehicle body; a wafer box lifting table is mounted on the frame; and the wafer box tray is fixed at the top of the wafer box lifting table. The wafer box carrier vehicle and the wafer box automatic positioning mechanism thereof can realize automatic positioning according to different wafer sizes in replacement of wafer boxes.