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Deep learning models have achieved promising disease prediction performance of the Electronic Health Records (EHR) of patients. However, most models developed under the I.I.D. hypothesis fail to consider the agnostic distribution shifts, diminishing the generalization ability of deep learning models to Out-Of-Distribution (OOD) data. In this setting, spurious statistical correlations that may change in different environments will be exploited, which can cause sub-optimal performances of deep learning models. The unstable correlation between procedures and diagnoses existed in the training distribution can cause spurious correlation between historical EHR and future diagnosis. To address this problem, we propose to use a causal representation learning method called Causal Healthcare Embedding (CHE). CHE aims at eliminating the spurious statistical relationship by removing the dependencies between diagnoses and procedures. We introduce the Hilbert-Schmidt Independence Criterion (HSIC) to measure the degree of independence between the embedded diagnosis and procedure features. Based on causal view analyses, we perform the sample weighting technique to get rid of such spurious relationship for the stable learning of EHR across different environments. Moreover, our proposed CHE method can be used as a flexible plug-and-play module that can enhance existing deep learning models on EHR. Extensive experiments on two public datasets and five state-of-the-art baselines unequivocally show that CHE can improve the prediction accuracy of deep learning models on out-of-distribution data by a large margin. In addition, the interpretability study shows that CHE could successfully leverage causal structures to reflect a more reasonable contribution of historical records for predictions.