The motor imagery (MI) based brain-computer interfaces (BCIs) have been proposed as a potential physical rehabilitation technology. However, the low classification accuracy achievable with MI tasks is still a challenge when building effective BCI systems. We propose a novel MI classification model based on measurement of functional connectivity between brain regions and graph theory. Specifically, motifs describing local network structures in the brain are extracted from functional connectivity graphs. A graph embedding model called Ego-CNNs is then used to build a classifier, which can convert the graph from a structural representation to a fixed-dimensional vector for detecting critical structure in the graph.We validate our proposed method on four datasets, and the results show that our proposed method produces high classification accuracies in two-class classification tasks (92.8% for dataset 1, 93.4% for dataset 2, 96.5% for dataset 3, and 80.2% for dataset 4) and multiclass classification tasks (90.33% for dataset 1). Our proposed method achieves a mean Kappa value of 0.88 across nine participants, which is superior to other methods we compared it to. These results indicate that there is a local structural difference in functional connectivity graphs extracted under different motor imagery tasks. Our proposed method has great potential for motor imagery classification in future studies.