A substrate processing apparatus includes; a carrier block; a first processing block including first lower and upper processing blocks to deliver a substrate to and from the carrier block; a second processing block including second lower and upper processing blocks provided adjacent to the first lower and upper processing blocks; a relay block including a lifting and transferring mechanism that delivers the substrate between the second lower and upper processing blocks; a controller that controls an operation of each main transfer mechanism such that one of upper and lower processing blocks forms an outward path through which the substrate is transferred from the carrier block to the relay block and the other forms a return path through which the substrate is transferred from the relay block to the carrier block; and a bypass transfer mechanism provided for each of the first and second processing blocks.