The ultrasonic motor (USM) is peculiarly prone to failure due to continuous high-frequency friction-related power transfer, whose failure mechanisms are remarkably different from traditional induction motors. Intelligent fault diagnosis provides a way to alarm and avoid catastrophic losses proactively. However, previous studies using deep learning usually ignore the inherent geometric structure of the signal distribution. This paper proposes an intelligent multi-signal fault diagnosis framework for USMs to restore the linear or nonlinear manifold structure by preserving the internal structure by integrating graph regularization with deep neural networks. Firstly, the one-dimensional CNN to learn spatial correlations and BiLSTM to exploit temporal dependencies are coalesced to build the deep neural network. Then, an improved k-nearest neighbor graph is proposed to protect the geometric structure information and force the latent features to be more concentrated within their classes. Moreover, the layer in the deep architecture to integrate graph regularization is designed to reduce computation cost, and an adaptive decay strategy is considered to adjust the coefficient of graph regularized automatically. A two-stage training algorithm is developed by considering the time to calculate the graph regularization term. Finally, the proposed multi-signal fault diagnosis framework is validated using datasets from the fault injection experiment of similar USMs in China’s Yutu rover of Chang’e lunar probe. Experimental results show that the proposed method can effectively discriminate different fault types.