A sampling phase difference compensation apparatus includes a signal generator, a signal analyzer and a compensator. The signal generator generates a first signal and a second signal, and outputs the first and second signals to a first path in a first time interval and a second path in a second time interval, respectively. The signal analyzer receives a transmitted first signal from the first path and a transmitted second signal from the second path, and performs a predetermined calculation on the transmitted first and second signals to determine a phase difference relationship, which is associated with a frequency-dependent phase difference and a sampling phase difference, between the transmitted first and second signals. The transmitted first signal is associated with the first signal, and the transmitted second signal is associated with the second signal. The compensator performs a phase difference compensation according to the phase difference relationship.