Provided is a wafer processing apparatus including a plate having a plurality of support pins configured such that a wafer is mounted on the plurality of support pins and a plurality of vacuum ports positioned between the plurality of support pins, a heater configured to heat the plate, a flow regulator configured to provide a vacuum pressure for fixing the wafer to the plurality of vacuum ports, and configured to adjust a flow rate of a fluid flowing into the plurality of vacuum ports to be a target flow rate, and a chuck controller configured to control the target flow of the fluid set in the flow regulator, wherein the chuck controller is configured to generate a flow control signal for reducing the target flow rate of the fluid and send the flow control signal to the flow regulator during a heating process of the wafer.