A cell controller controls the operation of a transport robot to keep a substrate belonging to a succeeding lot carried into a heating part in the fourth transport cycle from being transported out of the heating part in the next or fifth transport cycle, thereby preventing interference between the transport of substrates belonging to the succeeding lot and the transport of substrates belonging to a preceding lot. If interference is likely to occur between the transport of the substrates belonging to the succeeding lot and the transport of the substrates belonging to the preceding lot, the cell controller causes the substrates belonging to the succeeding lot not to be transported but to remain in processing units. This allows the transport of the substrates belonging to the succeeding lot in consideration of only the next transport cycle.