A substrate processing system includes a first chamber, a second chamber, and a cooling passage. The first chamber has therein a space for processing a substrate transferred from a first transfer chamber maintained in a vacuum atmosphere. The second chamber is disposed below the first chamber to be vertically aligned with the first chamber and configured to communicate with the first transfer chamber and a second transfer chamber maintained in an atmospheric atmosphere. The second chamber has substantially the same footprint as a footprint of the first chamber. Further, a cooling passage is disposed between the first chamber and the second chamber and configured to allow a coolant to flow therethrough.