The electronic reconnaissance system is the operational guarantee and premise of electronic warfare. It is an important tool for intercepting radar signals and providing intelligence support for sensing the battlefield situation. In this paper, a radar waveform automatic identification system for detecting, tracking and locating low probability interception (LPI) radar is studied. The recognition system can recognize 12 different radar waveform: binary phase shift keying (Barker codes modulation), linear frequency modulation (LFM), Costas codes, polytime codes (T1, T2, T3, and T4), and polyphase codes (comprising Frank, P1, P2, P3 and P4). First, the system performs time–frequency transform on the LPI radar signal to obtain a two-dimensional time–frequency image. Then, the time–frequency image is preprocessed (binarization and size conversion). The preprocessed time–frequency image is then sent to the convolutional neural network (CNN) for training. After the training is completed, the features of the fully connected layer are extracted. Finally, the feature is sent to the tree structure-based machine learning process optimization (TPOT) classifier to realize offline training and online recognition. The experimental results show that the overall recognition rate of the system reaches 94.42% when the signal-to-noise ratio (SNR) is −4 dB.