A semiconductor device manufacturing apparatus and a control method thereof which can shorten the manufacturing term of semiconductor devices are achieved. The semiconductor device manufacturing apparatus includes a plurality of processing apparatuses for taking out and processing semiconductor wafers successively which constitute a process lot, and including a standby port where a lot to be processed following processing of the process lot is put on standby. The semiconductor device manufacturing apparatus further includes a stocker for storing a lot to be transported to the standby port. According to the control method of the semiconductor device manufacturing apparatus, it is predicted when there is no standby wafer left in the processing apparatus in a prediction step. The predicted time is used to set transfer starting time when transfer of the next-processed lot to the standby port is started in a time setting step. A lot to be processed next is selected in a lot selecting step. The next-processed lot is transported to the processing apparatus at or after the transfer starting time in a transfer step.