Accurate 3D pre-operative planning shows significance of improving the precision of Total Hip Arthroplasty (THA) and Total Knee Arthroplasty (TKA). Since CT acquisition leads to high radiation exposure to patients, it is clinically desirable to find an alternative to CT scan for planning THA or TKA such as patient-specific 2D–3D reconstruction from a limited number of 2D calibrated X-ray images acquired with much lower radiation dose e.g. EOS imaging. Feature-based 2D–3D non-rigid registration based on the construction of statistical shape model (SSM) as a priori has been applied to reconstruct the surface models of proximal femur, and also the surface reconstruction of lower extremity for TKA has been validated in a cadaveric study by Zheng et al. On the other hand, intensity-based 2D–3D non-rigid registration can reconstruct the patient-specific intensity volumes like CTs to allow an insight into lower extremity morphology such as intramedullary anatomy, which can provide more comprehensive information in routine clinical practice. In this study, we will present an atlas- based 2D–3D reconstruction method and introduce its application to reconstruct the intensity volumes of lower extremity. Moreover, we take the articulation in the knee joint into consideration so as to avoid the penetration between femur and tibia which is favourable for the pre-operative planning. The results of the experiments demonstrated the efficacy of the proposed method on reconstructing the lower extremity morphology as well as the intramedullary canal anatomy.