In this paper, we propose a signature based pruning technique to facilitate the debugging of multi-threaded processors. To accomplish this, a pipelined implementation of the multi-threaded processor model is checked for correspondence against the specification model based on flushing proof. Then, a two-stage signature oriented pruning method is proposed to avoid the space explosion problem caused by inserting debugging facilities in the model. The results show an average improvement of 47%, and 71% in the size of decision formula and CPU time for the DLX processor, respectively.