Link scheduling in device-to-device (D2D) networks is usually formulated as a non-convex combinatorial problem, which is generally NP-hard and difficult to get the optimal solution. Traditional methods to solve this problem are mainly based on mathematical optimization techniques, where accurate channel state information (CSI), usually obtained through channel estimation and feedback, is needed. To overcome the high computational complexity of the traditional methods and eliminate the costly channel estimation stage, machine leaning (ML) has been introduced recently to address the wireless link scheduling problems. In this paper, we propose a novel graph embedding based method for link scheduling in D2D networks. We first construct a fully-connected directed graph for the D2D network, where each D2D pair is a node while interference links among D2D pairs are the edges. Then we compute a low-dimensional feature vector for each node in the graph. The graph embedding process is based on the distances of both communication and interference links, therefore without requiring the accurate CSI. By utilizing a multi-layer classifier, a scheduling strategy can be learned in a supervised manner based on the graph embedding results for each node. We also propose an unsupervised manner to train the graph embedding based method to further reinforce the scalability and generalizability and develop a K-nearest neighbor graph representation method to reduce the computational complexity. Extensive simulation demonstrates that the proposed method is near-optimal compared with the existing state-of-art methods but is with only hundreds of training samples. It is also competitive in terms of scalability and generalizability to more complicated scenarios.