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Recent literature focuses on utilizing the entity information in the sentence-level relation extraction (RE), but this risks leaking superficial and spurious clues of relations. As a result, RE still suffers from unintended entity bias, i.e., the spurious correlation between entity mentions (names) and relations. Entity bias can mislead the RE models to extract the relations that do not exist in the text. To combat this issue, some previous work masks the entity mentions to prevent the RE models from overfitting entity mentions. However, this strategy degrades the RE performance because it loses the semantic information of entities. In this paper, we propose the CORE (Counterfactual Analysis based Relation Extraction) debiasing method that guides the RE models to focus on the main effects of textual context without losing the entity information. We first construct a causal graph for RE, which models the dependencies between variables in RE models. Then, we propose to conduct counterfactual analysis on our causal graph to distill and mitigate the entity bias, that captures the causal effects of specific entity mentions in each instance. Note that our CORE method is model-agnostic to debias existing RE systems during inference without changing their training processes. Extensive experimental results demonstrate that our CORE yields significant gains on both effectiveness and generalization for RE. The source code is provided at: https://github.com/vanoracai/CoRE.