Label-efficient scene segmentation aims to achieve effective per-pixel classification with reduced labeling effort. Recent approaches for this task focus on leveraging unlabelled images by formulating consistency regularization or pseudo labels for individual pixels. Yet most of these methods ignore the 3D geometric structures naturally conveyed by image scenes, which is free for enhancing training segmentation models with better discrimination of image details. In this work, we present a novel Geometric Structure Refinement (GSR) framework to explicitly exploit the geometric structures of image scenes to enhance the semi-supervised training of segmentation models. In the training phase, we generate initial dense pseudo labels based on fast and coarse annotations, and then utilize the free unsupervised 3D reconstruction of the image scene to calibrate the dense pseudo labels with more reliable details. With the calibrated pseudo groundtruth, we are able to conveniently train any existing image segmentation models without increasing the costs of annotations or modifying the models' architectures. Moreover, we explore different strategies for allocating labeling effort in semi-supervised scene segmentation, and find that a combination of finely-labeled samples and coarsely-labeled samples performs better than the traditional dense-fine only annotations. Extensive experiments on datasets including Cityscapes and KITTI are conducted to evaluate our proposed methods. The results demonstrate that GSR can be easily applied to boost the performance of existing models like PSPNet, DeepLabv3+, etc with reduced annotations. With half of the annotation effort, GSR achieves 99% of the accuracy of its fully supervised state-of-the-art counterparts.