A temperature controller for a semiconductor wafer is configured to perform a temperature control on a plurality of temperature adjusters including a reference temperature adjuster to perform a temperature adjustment of the semiconductor wafer, in which a manipulated variable calculator to give a manipulated variable to a master loop and a slave loop includes a master-slave switching unit configured to switch between the master loop and the slave loop and a master-slave cancellation unit configured to cancel a setting of the master loop and the slave loop when a temperature setpoint of the slave loop is set to have a temperature gradient against a temperature setpoint of the master loop.