We present a Fourier-domain filtering method for charge-coupled device (CCD)-based thermoreflectance microscopy to improve the thermal imaging speed while maintaining high thermal sensitivity. The time-varying reflected light distribution from the surface of bias-modulated microresistor was recorded by a CCD camera in free-run mode and converted to the frequency domain using the fast Fourier transform (FFT) for all pixels of the CCD. After frequency peak filtering followed by inverse FFT, a thermoreflectance image was obtained. The imaging results of the proposed method were quantitatively compared with those of the conventional four-bucket method, showing that the Fourier-domain filtering method can provide thermal imaging 24-42 times faster than the four-bucket method, depending on the required thermal sensitivity.