Recently, many researchers have concentrated on distant supervision relation extraction (DSRE). DSRE has solved the problem of the lack of data for supervised learning, however, the data automatically labeled by DSRE has a serious problem, which is class imbalance. The data from the majority class obviously dominates the dataset, in this case, most neural network classifiers will have a strong bias towards the majority class, so they cannot correctly classify the minority class. Studies have shown that the degree of separability between classes greatly determines the performance of imbalanced data. Therefore, in this paper we propose a novel model, which combines class-to-class separability and cost-sensitive learning to adjust the maximum reachable cost of misclassification, thus improving the performance of imbalanced data sets under distant supervision. Experiments have shown that our method is more effective for DSRE than baseline methods. © 2019 Tech Science Press. All rights reserved.