The magnetotelluric (MT) data collected in an ore-concentration area are extremely vulnerable to all kinds of noise pollution. However, separating real MT signals from strong noise is still a difficult problem, and the noise in MT data is quite distinct from clean data in morphological features. By performing the signal-noise identification and data prediction, we develop a deep learning method to denoise MT data containing strong noise. First, we use the convolutional neural network (CNN) to learn the feature differences between the samples of massive noise and clean data and use the learned features to realize signal-noise identification of the measured data. Second, we use the measured clean data obtained by CNN identification to train the long short-term memory (LSTM) neural network and perform the prediction denoising of the noisy data. The simulation results clearly demonstrate the following two facts: (1) the predicted data output from LSTM basically matches the time-frequency domain features of the real data and (2) our CNN method performs significantly better than the features parameter classification method in dealing with signal-noise identification. In addition, the validity of our method is verified by the processing results of the measured data.