Recovering 3D structures from the monocular image sequence is an inherently ambiguous problem that has attracted considerable attention from several research communities. To resolve the ambiguities, a variety of additional priors, such as low-rank shape basis, have been proposed. In this paper, we make two contributions. First, we introduce an assumption that 3D structures lie on the union of nonlinear subspaces. Based on this assumption, we propose a Non-Rigid Structure from Motion (NRSfM) method with kernelized low-rank representation. To be specific, we utilize the soft-inextensibility constraint to accurately recover 3D human motions. Second, we extend this NRSfM method to the marker-less 3D human pose estimation problem by combining with Convolutional Neural Network (CNN) based 2D human joint detectors. To evaluate the performance of our methods, we apply our marker-based method on several sequences from Utrecht Multi-Person Motion (UMPM) benchmark and CMU MoCap datasets, and then apply the marker-less method on the Human3.6M datasets. The experiments demonstrate that the kernelized low-rank representation is more suitable for modeling the complex deformation and the method consequently yields more accurate reconstructions. Benefiting from the CNN-based detector, the marker-less approach can be applied to more real-life applications.