As a new type of manufacturing equipment, redundant hybrid machines have the theoretical advantage over the traditional serial machines in efficiently processing large structural parts with high material removal ratio and complex parts with curved surfaces. In order to solve the accuracy problem of the redundantly actuated spatial parallel module of a five-axis hybrid machine, an improved kinematic calibration method is proposed in this article. First, different from error modeling for the corresponding non-redundant parallel module, the geometric error model of the redundantly actuated spatial parallel module considers the deformations at active joints caused by actuation redundancy as an error source. Then, the applicable error model is developed using projection technique to remove the need of active joints’ stiffness measurement or modeling. Later, the practical error model is derived from model reduction method to avoid using additional sensors or gratings. Finally, three forms of relative measurement and step identification are adopted for the calibration work, and the bilinear interpolation compensation function is introduced to ensure the calibration effect. On this basis, the kinematic calibration of the redundantly actuated spatial parallel module is conducted. The max position errors are reduced from original −0.192 to 0.075 mm after RM1 and SI1, and then further reduced to 0.014 mm after bilinear interpolation compensation, while the max orientation errors are reduced from −0.017° and 0.249° to −0.005° and −0.007° after RM2 and SI2, and RM3 and SI3, respectively. A contrasting experiment is also carried out with the previous method for the corresponding non-redundant parallel module. As a result, the proposed method shows better convergence value and speed in identifying error parameters, and therefore the effectiveness and efficiency of the proposed method for the redundantly actuated spatial parallel module are validated.