In a method of manufacturing a semiconductor device of an embodiment, at room temperature, a first substrate including a semiconductor laminate body is adhered to a second substrate with a smaller thermal expansion coefficient than that of the first substrate. Then, the first substrate and the second substrate are heated with the first substrate heated at a temperature higher than that of the second substrate. Thus the first substrate and the second substrate are bonded together. The first substrate is either a sapphire substrate including a nitride-based semiconductor layer, or a GaAs substrate including a phosphorus-based semiconductor layer. The second substrate is a silicon substrate, a GaAs substrate, a Ge substrate, or a metal substrate.