Heterogeneous face recognition (HFR) aims to match facial images acquired from different sensing modalities with mission-critical applications in forensics, security and commercial sectors. However, HFR is a much more challenging problem than traditional face recognition because of large intra-class variations of heterogeneous face images and limited training samples of cross-modality face image pairs. This paper proposes a novel approach namely Wasserstein CNN (convolutional neural networks, or WCNN for short) to learn invariant features between near-infrared and visual face images (i.e. NIR-VIS face recognition). The low-level layers of WCNN are trained with widely available face images in visual spectrum. The high-level layer is divided into three parts, i.e., NIR layer, VIS layer and NIR-VIS shared layer. The first two layers aims to learn modality-specific features and NIR-VIS shared layer is designed to learn modality-invariant feature subspace. Wasserstein distance is introduced into NIR-VIS shared layer to measure the dissimilarity between heterogeneous feature distributions. So W-CNN learning aims to achieve the minimization of Wasserstein distance between NIR distribution and VIS distribution for invariant deep feature representation of heterogeneous face images. To avoid the over-fitting problem on small-scale heterogeneous face data, a correlation prior is introduced on the fully-connected layers of WCNN network to reduce parameter space. This prior is implemented by a low-rank constraint in an end-to-end network. The joint formulation leads to an alternating minimization for deep feature representation at training stage and an efficient computation for heterogeneous data at testing stage. Extensive experiments on three challenging NIR-VIS face recognition databases demonstrate the significant superiority of Wasserstein CNN over state-of-the-art methods.