Purpose We aim to quantitatively characterise the knee joint function in vivo under body-weight-bearing conditions via subject-specific models extracted from magnetic resonance (MR) data, in order to better understand the knee joint kinematic function in 3D. Methods Six healthy volunteers without any record of knee abnormality were scanned using a combined MR imaging strategy to record quasi-squatting motion and 3D knee anatomy. After a semi-automatic segmentation to delineate tibio-femoral articulation components, motion data were mapped to the anatomical data using a bi-rigid registration in order to achieve six degrees of freedom. The individual knee joint function was characterised by analysing the tibio-femoral articulation contact mechanism based on the reconstructed models in 3D and MR images in 2D. Contact points were extracted and their trajectory was plotted on the tibia plateau. Results The 3D models clearly show the relative rotation and gliding between tibia and femur during global flexion. Within the measured flexion arc, the contact points move less between 30∘ and 100∘ on both tibial plateaux as compared to that on the rest of the flexion arc. Four out of the six volunteers showed a global pattern of less moving extent of contact points on the medial tibial plateau than on the lateral tibial plateau in both 3D and 2D. Conclusion The proposed subject-specific model is able to characterise knee joint kinematic function. It provides a way to describe knee joint surface kinematics quantitatively, which may help to better understand the knee function and joint derangements.