With the progress of signal processing technology and the emergence of new system radars, the space electromagnetic environment becomes more and more complex, which puts forward higher requirements for the deinterleaving method of radar signals. Traditional signal deinterleaving algorithms rely heavily on manual experience threshold and have poor robustness. To address this problem, we designed an intelligent radar signal deinterleaving algorithm that was completed by encoding the frequency characteristic matrix and semantic segmentation network, named Sep-RefineNet. The frequency characteristic matrix can well construct the semantic features of different pulse streams of radar signals. The Sep-RefineNet semantic segmentation network can complete pixel-level segmentation of the frequency characteristic matrix and finally uses position decoding and verification to obtain the position in the original pulse stream to complete radar signals deinterleaving. The proposed method avoids the processing of threshold judgment and pulse sequence search in traditional methods. The results of the experiment show that this algorithm improves the deinterleaving accuracy and has a good against-noise ability of aliasing pulses and missing pulses