Kinematic calibration plays an important role in the improvement of positioning accuracy for parallel manipulators. Based on the specific geometric constraints of limbs, this paper presents a new kinematic parameter identification method for the widely studied 3-PRS parallel manipulator. In the proposed calibration method, the planes where the PRS limbs exactly located are identified firstly as the geometric characteristics of the studied parallel manipulator. Then, the limbs can be considered as planar PR mechanisms whose kinematic parameters can be determined conveniently according to the limb planes identified in the first step. The main merit of the proposed calibration method is that the system error model which relates the manipulator’s kinematic errors to the output ones is not required for kinematic parameter identification. Instead, only two simple geometric problems need to be established for identification, which can be solved readily using gradient-based searching algorithms. Hence, another advantage of the proposed method is that parameter identification of the manipulator’s limbs can be accomplished individually without interactive impact on each other. In order to validate the effectiveness and efficiency of the proposed method, calibration experiments are conducted on an apparatus of the studied 3-PRS parallel manipulator. The results show that using the proposed two-step calibration method, the kinematic parameters can be identified quickly by means of gradient searching algorithm (converge within five iterations for both steps). The positioning accuracy of the studied 3-PRS parallel manipulator has been significantly improved by compensation according to the identified parameters. The mean position and orientation errors at the validation configurations have been reduced to 1.56 × 10−4 m and 1.13 × 10−3 rad, respectively. Further, the proposed two-step kinematic calibration method can be extended to other limited-degree-of-freedom parallel manipulators, if proper geometric constraints can be characterized for their kinematic limbs.