Graph shift regularization is a new and effective graph-based semi-supervised classification method, but its performance is closely related to the representation graphs. Since directed graphs can convey more information about the relationship between vertices than undirected graphs, an intelligent method called graph shift regularization with directed graphs (GSR-D) is presented for fault diagnosis of rolling bearings. For greatly improving the diagnosis performance of GSR-D, a directed and weighted k-nearest neighbor graph is first constructed by treating each sample (i.e., each vibration signal segment) as a vertex, in which the similarity between samples is measured by cosine distance instead of the commonly used Euclidean distance, and the edge weights are also defined by cosine distance instead of the commonly used heat kernel. Then, the labels of samples are considered as the graph signals indexed by the vertices of the representation graph. Finally, the states of unlabeled samples are predicted by finding a graph signal that has minimal total variation and satisfies the constraint given by labeled samples as much as possible. Experimental results indicate that GSR-D is better and more stable than the standard convolutional neural network and support vector machine in rolling bearing fault diagnosis, and GSR-D only has two tuning parameters with certain robustness.