The received signal in through-transmission ultrasound measurements of cancellous bone consists of two longitudinal waves, called the fast and slow waves. Analysis of these fast and slow waves may reveal characteristics of the cancellous bone that would be good indicators of osteoporosis. Because the two waves often overlap, decomposition of the received signal is an important problem in the characterization of bone quality. This study proposes a fast and accurate decomposition method based on the frequency domain interferometry imaging method with a modified wave transfer function that uses a phase rotation parameter. The proposed method accurately characterized the fast and slow waves in the experimental study, and the residual intensity, which was normalized with respect to the received signal intensity, was less than -20 dB over the bone specimen thickness range from 6 to 15 mm. In the simulation study, the residual intensity was less than -20 dB over the specimen thickness range from 3 to 8 mm. Decomposition of a single received signal takes only 5 s using a laptop personal computer with a single central processing unit. The proposed method has great potential to provide accurate and rapid measurements of indicators of osteoporosis in cancellous bone.