Deep learning models are the state of the art for semantic segmentation of point clouds, the success of which relies on the availability of large-scale annotated datasets. However, it can be prohibitively costly to prepare such datasets. In this work, we propose a holistic active learning (AL) approach to maximize model performance given limited annotation budgets. We investigate the appropriate sample granularity for active selection under the realistic “click” measurement of annotation cost, and demonstrate that superpoint-based selection allows for most efficient usage of the limited budget, when compared with point-level, polygon-level and instance/shape-level selection. We further propose new objective for AL acquisition function and exploit local consistency constraints to boost the performance of our superpoint-based approach. We evaluate our methods on three benchmark datasets, ShapeNet and PartNet and S3DIS. The results demonstrate that AL is an effective strategy to address the high annotation costs in semantic point cloud segmentation.