Emotion classification based on neurophysiology signals has been a challenging issue in the literature. Recent neuroscience findings suggest that brain network structure underlying the different emotions provides a window in understanding human affection. In this paper, we propose a novel method to capture the distinct minimum spanning tree (MST) topology underpinning the different emotions. Specifically, we propose a hierarchical aggregation-based graph neural network to investigate the MST structure in emotion recognition. Extensive experiments on the public available DEAP dataset demonstrate the superior performance of the model in emotion classification as compared to existing methods. In addition, the results show that the theta, lower beta and gamma frequency band network information are more sensitive to emotions, suggesting a multi-frequency interaction in emotion processing.