To provide a temperature control apparatus for a microchip that accurately and locally controls the temperature of a specific part of the microchip intended for the temperature control.

The temperature control apparatus 10 comprises a temperature control unit 20 supported by an elastomer 23 so as to be able to move three-dimensionally relative to a microchip 30 and pushed against the surface 30a of the microchip 30. Thereby the temperature control unit 20 moves along the shape of the microchip 30 to come in close contact with the microchip 30 at a predetermined position even when the contact surface 201 of the temperature control unit 20 and the specific part of the microchip 30 intended for the temperature control do not exist on a uniform plane or the microchip 30 is warped. The elastomer 23 is disposed between a Peltier device 21 and a heat sink 22. The elastomer 23 is made from a material having good heat conductivity such as a silicone resin and therefore the waste heat coming out of the Peltier device 21 is discharged to the heat sink 22 via the elastomer 23.