To provide a wafer joining apparatus capable of absorbing variations in the thickness of a wafer, by changing the shape of a pressing surface so as to raise flatness of a wafer joining surface.

This wafer joining apparatus has top plates for holding wafers respectively, a pressing profile control module having a hollow part into which gas or liquid is injected, a transmission member for transmitting the surface shape change of the pressing profile control module to the surfaces of the top plates, a heater part for heating, a cooing part for cooling the heater for heating, and a pressing unit for pressing the wafers through the pressing profile control module. The pressing unit includes one cylinder into which gas or liquid is injected, and the wafer joining apparatus also has a control part for controlling the pressure of the gas or liquid injected into the hollow part and the pressure of the gas or liquid injected into the cylinder.