Panoramic image enables deeper understanding and more holistic perception of 360-degree surrounding environment, which can naturally encode enriched scene context information compared to standard perspective image. Previous work has made lots of effort to solve the scene understanding task in a hybrid solution based on 2D-3D geometric reasoning, thus each sub-task is processed separately and few correlations are explored in this procedure. In this paper, we propose a fully 3D method for holistic indoor scene understanding which recovers the objects' shapes, oriented bounding boxes and the 3D room layout simultaneously from a single panorama. To maximize the exploration of the rich context information, we design a transformer-based context module to predict the representation and relationship among each component of the scene. In addition, we introduce a new dataset for scene understanding, including photo-realistic panoramas, high-fidelity depth images, accurately annotated room layouts, oriented object bounding boxes and shapes. Experiments on the synthetic and new datasets demonstrate that our method outperforms previous panoramic scene understanding methods in terms of both layout estimation and 3D object detection.