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Graph neural networks (GNNs) have attracted significant interest recently since they can effectively process and analyze graph-structured data commonly found in real-world applications. However, the predicament that GNNs are difficult to train becomes worse as the layers increase. The essence of this problem is that stacking layers will reduce the stability of forward propagation and gradient back-propagation. And as the increasing scale of models (measured by the number of parameters), how to efficiently and effectively adapt it to particular downstream tasks becomes an intriguing research issue. In this work, motivated by the effect of orthogonality constraints, we propose a simple orthogonal training framework to impose the orthogonality constraints on GNNs, which can help models find a solution vector in a specific low dimensional subspace and stabilize the signaling processes at both the forward and backward directions. Specifically, we propose a novel polar decomposition-based orthogonal initialization (PDOI-R) algorithm, which can identify the low intrinsic dimension within the Stiefel Manifold and stabilize the training process. Extensive experiments demonstrate the effectiveness of the proposed method in multiple downstream tasks, showcasing its generality. The simple method can help existing state-of-the-art models achieve better performance.