Large language models (LLMs) have shown impressive performance on downstream tasks through in-context learning (ICL), which heavily relies on the demonstrations selected from annotated datasets. Existing selection methods may hinge on the distribution of annotated datasets, which can often be long-tailed in real-world scenarios. In this work, we show that imbalanced class distributions in annotated datasets significantly degrade the performance of ICL across various tasks and selection methods. Moreover, traditional rebalance methods fail to ameliorate the issue of class imbalance in ICL. Our method is motivated by decomposing the distributional differences between annotated and test datasets into two-component weights: class-wise weights and conditional bias. The key idea behind our method is to estimate the conditional bias by minimizing the empirical error on a balanced validation dataset and to employ the two-component weights to modify the original scoring functions during selection. Our approach can prevent selecting too many demonstrations from a single class while preserving the effectiveness of the original selection methods. Extensive experiments demonstrate the effectiveness of our method, improving the average accuracy by up to 5.46 on common benchmarks with imbalanced datasets.