Feature extraction is an important process for the automatic recognition of synthetic aperture radar targets, but the rising complexity of the recognition network means that the features are abstractly implied in the network parameters and the performances are difficult to attribute. We propose the modern synergetic neural network (MSNN), which transforms the feature extraction process into the prototype self-learning process by the deep fusion of an autoencoder (AE) and a synergetic neural network. We prove that nonlinear AEs (e.g., stacked and convolutional AE) with ReLU activation functions reach the global minimum when their weights can be divided into tuples of M-P inverses. Therefore, MSNN can use the AE training process as a novel and effective nonlinear prototypes self-learning module. In addition, MSNN improves learning efficiency and performance stability by making the codes spontaneously converge to one-hots with the dynamics of Synergetics instead of loss function manipulation. Experiments on the MSTAR dataset show that MSNN achieves state-of-the-art recognition accuracy. The feature visualization results show that the excellent performance of MSNN stems from the prototype learning to capture features that are not covered in the dataset. These representative prototypes ensure the accurate recognition of new samples.