A signal comparison apparatus and a method of controlling the same are provided. The signal comparison apparatus includes a first comparator, a self-timed clock generator and a controller. The first comparator is controlled by a start signal to compare differences of first input signals and generate output signals. The self-timed clock generator receives the output signals to generate a self-timed clock signal. The controller receives the self-timed clock signal and calculates a time interval of the self-timed clock signal which responds to the first input signals of the first comparator, and determines whether the time interval is equal to or larger than a threshold time to generate a metastable detection signal. When the time interval is equal to or larger than the threshold time, the controller outputs the metastable detection signal as the start signal, such that the first comparator continue comparing the next differences of the first input signals.