Nowadays integrated circuits (ICs) are underpinning all major information technology innovations including the current trends of artificial intelligence (AI). Modern IC designs often involve analyses of complex phenomena (such as timing, noise, and power etc.) for tens of billions of electronic components, like resistance (R), capacitance (C), transistors and gates, interconnected in various complex structures. Those analyses often need to strike a balance between accuracy and speed as those analyses need to be carried out many times throughout the entire IC design cycles. With the advancement of AI, researchers also start to explore new ways in leveraging AI to improve those analyses. This paper focuses on one of the most important analyses, timing analysis for interconnects. Since IC interconnects can be represented as an RC-tree, a specialized graph as tree, we design a novel tree-based graph neural network, SyncTREE, to speed up the timing analysis by incorporating both the structural and physical properties of electronic circuits. Our major innovations include (1) a two-pass message-passing (bottom-up and top-down) for graph embedding, (2) a tree contrastive loss to guide learning, and (3) a closed formula-based approach to conduct fast timing. Our experiments show that, compared to conventional GNN models, SyncTREE achieves the best timing prediction in terms of both delays and slews, all in reference to the industry golden numerical analyses results on real IC design data.