Using the macro-micro combination positioning system for nanomanipulating can fulfill the requirements of large workspace, high precision and multi-degrees of freedom. As a macro part of the macro-micro combination positioning system, a redundantly actuated three degrees-of-freedom (DOF) parallel kinematic mechanism (4ṞRR) with a directly driven system is studied in this paper. Firstly, the error sensitivity of the 4ṞRR planar parallel mechanism is analyzed with global errors sensitive index (GESI) based on the error model of the positioning system. Then, a novel and practical calibration method combined with an error compensation strategy is proposed for the 4ṞRR positioning system. Finally, in order to verify the proposed method, a series of experiments are conducted with the laser measurement system in creditable conditions, and the data are illustrated for comparisons. The experimental results show that the positioning accuracy of the 4ṞRR positioning system is improved, and the performances of the end-effector are enhanced based on the proposed method.