The invention discloses a clustering-based overlapping signal elimination method and a system. The method comprises steps of acquiring data received by sliding windows; through sliding of the sliding windows on a time axis, collecting signals received in a corresponding time period; carrying out clustering on the data according to amplitude values so as to obtain clusters in different amplitude ranges; determining clusters to be basic or combined clusters according to average values of amplitude values in corresponding clusters, and if clusters are combined clusters, determining the combined relation between the combined clusters and the basic clusters; according to the combined relation between the combined cluster and the basic clusters, dividing data in the combined clusters into corresponding basic clusters; and splicing basic clusters in front and back sliding windows to obtain non-overlapping signals. According to the invention, overlapping signals formed by different types of pulse position modulation signals can be eliminated and the method and the system are universal.