Hand motion tracking is essential in many fields, e.g., immersive virtual reality, teleoperation of robotic hand, and hand rehabilitation of stroke patient, as human hand plays a crucial role in our daily life. The highly under-actuated hand exoskeleton, which can track the 6-DoF motions of each fingertip via a highly under-actuated kinematic chain, exhibits many benefits in wearability and portability over other solutions. However, due to the non-anthropomorphic linkage, this hand exoskeleton also encounters difficulties in measuring human-finger’s joint angles. While the joint-space is important in many scenarios, such as teleoperating a robotic hand with anthropomorphic kinematics but with different size to human. Here we proposed a new method to reconstruct the human finger joints by using a highly under-actuated hand exoskeleton. Our key contribution is the arc-fitting algorithm, which is able to calibrate the misalignment between the exoskeleton’s and the human-finger’s base frames and estimate the length of human’s phalanxes, by using the fingertip’s circular motions. With knowing the aforementioned informations, the joint angles can be reconstructed in high precision based on the inverse kinematics models of human fingers. Furthermore, our proposed method is compared with a baseline method, in which the joint angles obtained by a motion capture system are served as ground-truth. The results demonstrate that our proposed method exhibits excellent performance in reconstructing finger’s joint configurations.