The noise suppression method based on dictionary learning has shown great potential in magnetotelluric (MT) data processing. However, the constraints used in the existing algorithm’s method need to set manually, which significantly limits its application. To solve this problem, we propose a deep learning optimized dictionary learning denoising method. We use a deep convolutional network to learn the characteristic parameters of high-quality MT data independently and then use them as the constraints for dictionary learning so as to achieve fully adaptive sparse decomposition. The method uses unified parameters for all data and completely eliminates subjective bias, which makes it possible to batch-process MT data using sparse decomposition. The processing results of simulated and field data examples show that the new method has good adaptability and can achieve recognition with high accuracy. After processing with our method, the apparent resistivity and phase curves became smoother and more continuous, and the results were validated by the remote reference method. Our method can be an effective alternative method when no remote reference station is set up or the remote reference processing is not effective.