A selective microwave irradiation annealing method for the preparation of efficient polymer photovoltaic devices is reported. The power conversion efficiency of the devices increases upon increasing the irradiation time. In situ temperature probing suggests that the microwaves could penetrate the anode without any loss of energy, whereas the organic active layer and the cathode were both heated. Furthermore, X-ray diffraction indicated that microwave annealing enhanced the degree of crystallization of the polymer chains.