Accurate lower-limb pose estimation is aprerequisite of skeleton based pathological gait analysis. To achieve this goal in free-living environments for long-term monitoring, single depth sensor has been proposed in research. However, the depth map acquired from a single viewpoint encodes only partial geometric information of the lower limbs and exhibits large variations across different viewpoints. Existing off-the-shelf 3D pose tracking algorithms and public datasets for depth based human pose estimation are mainly targeted at activity recognition applications. They are relatively insensitive to skeleton estimation accuracy, especially at the foot segments. Furthermore, acquiring ground truth skeleton data for detailed biomechanics analysis also requires considerable efforts. To address these issues, we propose a novel cross-domain self-supervised complete geometric representation learning framework, with knowledge transfer from the unlabelled synthetic point clouds of full lower-limb surfaces. The proposed method can significantly reduce the number of ground truth skeletons (with only 1%) in the training phase, meanwhile ensuring accurate and precise pose estimation and capturing discriminative features across different pathological gait patterns compared to other methods.