Web Services Quality Prediction has become a popular research theme in Cloud Computing and the Internet of Things. Graph Convolutional Network (GCN)-based methods are more efficient by aggregating feature information from the local graph neighborhood. Despite the fact that these prior works have demonstrated better prediction performance, they are still challenged as follows: (1) first, the user-service bipartite graph is essentially a heterogeneous graph that contains four kinds of relationships. Previous GCN-based models have only focused on using some of these relationships. Therefore, how to fully mine and use the above relationships is critical to improving the prediction accuracy. (2) After the embedding is obtained from the GCNs, the commonly used similarity calculation methods for downstream prediction need to traverse the data one by one, which is time-consuming. To address these challenges, this work proposes a novel relationship discovery and hierarchical embedding method based on GCNs (named as RDHE), which designs a dual mechanism to represent services and users, respectively, designs a new community discovery method and a fast similarity calculation process, which can fully mine and utilize the relationships in the graph. The results of the experiment on the real data set show that this method greatly improved the accuracy of the web service quality prediction.