Recently, a signal sorting algorithm based on the congruence transform has been proposed, which is effective in dealing with the staggered Pulse Repetition Interval (PRI) signals. It can effectively sort the staggered PRI signals and obtain the sub-PRI sequence directly without sub-PRI ranking, and it is less affected by interfered pulses and pulse loss. Nevertheless, we find that the algorithm causes pseudo-peaks in the remainder histogram when sorting signals such as sliding PRI, sinusoidal PRI, etc. (collectively referred to as periodic PRI signal in this paper) and pseudo-peaks will cause errors in signal sorting. To solve the issue of pseudo-peaks when sorting periodic PRI signals, an improved sorting algorithm based on congruence transform is proposed. According to the analysis of the congruence characteristics of the periodic PRI signal, a novel method is proposed to identify pseudo-peaks based on the histogram peak amplitude and symmetric difference set. The signal sorting algorithm based on congruence transform is improved to achieve a good sorting effect on periodic PRI signals. Simulation experiments demonstrate that the novel algorithm can effectively sort periodic PRI signals and improve Precall, Pd, and Pf by 6.9%, 5.1%, and 3.2%, respectively, compared to the typical similar algorithms.