This paper investigates the indistinguishable points (difficult to predict label) in semantic segmentation for large-scale 3D point clouds. The indistinguishable points consist of those located in complex boundary, points with similar local textures but different categories, and points in isolate small hard areas, which largely harm the performance of 3D semantic segmentation. To address this challenge, we propose a novel Indistinguishable Area Focalization Network (IAF-Net), which select indistinguishable points adaptively by utilizing the hierarchical semantic features and enhance fine-grained features for points especially those indistinguishable points. We also introduce multi-stage loss to improve the feature representation in a progressive way. Moreover, in order to analyze the segmentation performances of indistinguishable areas, we propose a new evaluation metric called Indistinguishable Points Based Metric (IPBM). Our IAF-Net achieves the state-of-the-art performance on several popular 3D point datasets e.g. S3DIS and ScanNet, and clearly outperform other methods on IPBM. Our code will be available at https://github.com/MingyeXu/IAF-Net.