Representation learning is a fundamental but challenging problem, especially when the distribution of data is unknown. In this paper, we propose a new representation learning method, named Structure Transfer Machine (STM), which enables feature learning process to converge at the representation expectation in a probabilistic way. We theoretically show that such an expected value of the representation (mean) is achievable if the manifold structure can be transferred from the data space to the feature space. The resulting structure regularization term, named manifold loss, is incorporated into the loss function of the typical deep learning pipeline. The STM architecture is constructed to enforce the learned deep representation to satisfy the intrinsic manifold structure from the data, which results in robust features that suit various application scenarios, such as digit recognition, image classification and object tracking. Compared with state-of-the-art CNN architectures, we achieve better results on several commonly used public benchmarks.