We propose a Graph Neural Network (GNN)-based approach for Handwritten Mathematical Expression (HME) recognition by modeling HMEs as graphs, where nodes represent symbols and edges capture spatial dependencies. A deep BLSTM network is used for symbol segmentation, recognition, and spatial relation classification, forming an initial primitive graph. A 2D-CFG parser then generates all possible spatial relations, while the GNN-based link prediction model refines the structure by removing unnecessary connections, ultimately forming the Symbol Label Graph. Experimental results demonstrate the effectiveness of our approach, showing promising performance in HME structure recognition.