Abstract: To solve the jitter problem in separation with pulse interval distribution matrix (PIDM), an improved algorithm was proposed. Firstly, based on the idea of overlapping PRI boxes consulted from improving PRI transform, the sum of the amplitudes was used to substitute the main period line in the overlapping range of PRI boxes in PIDM matrix to carry out main, subsequence line and threshold calculation. And then, the calculation method of threshold was improved. Finally, the values that pass the threshold were clustered and analyzed, and the average value (subsequence extraction) or the minimum value (main period extraction) in the cluster was taken as the real PRI value. The research results show that the improved algorithm can provide a certain anti-jitter (5%~10%) on the basis of basically maintaining the success rate of the original algorithm, and can also adapt to the complex environment of multiple radiation sources.