An isothermal reactor in which reaction solutions can be controlled at constant temperature under constant microwave irradiation has been developed for investigating microwave effects on chemical reactions. A structure was devised in which a heat-transfer medium with a low dielectric loss factor, which hardly absorbs any microwaves, flowed outside a reaction tube, and the basic structure of the reactor was designed using electromagnetic simulation. In addition, the microwave effects on two reactions (homogeneous reaction and heterogeneous reaction) were investigated using the developed isothermal reactor. The Suzuki-Miyaura coupling reaction as a homogeneous reaction and the Sonogashira coupling reaction with solid palladium catalyst supported inside a reaction tube as a heterogeneous reaction have been examined. The results show that the yields obtained by microwave heating and oil-bath heating are almost equal, and thus microwaves have no effects in the homogeneous Suzuki-Miyaura coupling reaction experiment. On the other hand, the yield obtained by microwave heating is 2.4 times higher than that obtained by oil-bath heating in the heterogeneous Sonogashira coupling reaction experiment, in which the temperatures of reactant solutions in both microwave heating and oil-bath heating were kept at 373 K using the isothermal reactor. It is believed that palladium catalyst supported inside a reaction tube is heated locally by microwaves, which enhances the localized reaction rate and improves the yield. In addition, the temperature of the catalyst is inferred to be approximately 403 K by microwaves.