Conventional computer-assisted orthopaedic navigation systems rely on the tracking of dedicated optical markers for patient poses, which makes the surgical workflow more invasive, tedious, and expensive. Visual tracking has recently been proposed to measure the target anatomy in a markerless and effortless way, but the existing methods fail under real-world occlusion caused by intraoperative interventions. Furthermore, such methods are hardware-specific and not accurate enough for surgical applications. In this paper, we propose a RGB-D sensing-based markerless tracking method that is robust against occlusion. We design a new segmentation network that features dynamic region-of-interest prediction and robust 3D point cloud segmentation. As it is expensive to collect large-scale training data with occlusion instances, we also propose a new method to create synthetic RGB-D images for network training. Experimental results show that our proposed markerless tracking method outperforms recent state-of-the-art approaches by a large margin, especially when an occlusion exists. Furthermore, our method generalises well to new cameras and new target models, including a cadaver, without the need for network retraining. In practice, by using a high-quality commercial RGB-D camera, our proposed visual tracking method achieves an accuracy of 1-2 degress and 2-4 mm on a model knee, which meets the standard for clinical applications.