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Graph-based models have achieved great success in person re-identification tasks recently, which compute the graph topology structure (affinities) among different people first and then pass the information across them to achieve stronger features. But we find existing graph-based methods in the visible-infrared person re-identification task (VI-ReID) suffer from bad generalization because of two issues: 1) train-test modality balance gap, which is a property of VI-ReID task. The number of two modalities data are balanced in the training stage, but extremely unbalanced in inference, causing the low generalization of graph-based VI-ReID methods. 2) sub-optimal topology structure caused by the end-to-end learning manner to the graph module. We analyze that the well-trained input features weaken the learning of graph topology, making it not generalized enough during the inference process. In this paper, we propose a Counterfactual Intervention Feature Transfer (CIFT) method to tackle these problems. Specifically, a Homogeneous and Heterogeneous Feature Transfer (H2FT) is designed to reduce the train-test modality balance gap by two independent types of well-designed graph modules and an unbalanced scenario simulation. Besides, a Counterfactual Relation Intervention (CRI) is proposed to utilize the counterfactual intervention and causal effect tools to highlight the role of topology structure in the whole training process, which makes the graph topology structure more reliable. Extensive experiments on standard VI-ReID benchmarks demonstrate that CIFT outperforms the state-of-the-art methods under various settings.