The aeroengine industry has set strict upper limits for assembly errors in rotor-connecting processes, because assembly errors significantly affect aeroengine stability. Applications of multi-axis mechanisms have the potential to solve the low efficiency of traditional manual connection processes. However, multiple error sources are simultaneously introduced. Thus, an accurate prediction method of rotor assembly error considering multiple error sources is of vital importance, by which the applicability of the new mechanism to rotors can be tested. In this study, a new prediction method for rotor assembly errors is proposed based on the use of a novel multi-axis measuring and connecting mechanism. First, the error propagation among the rotor errors, measurement errors, mechanism errors, and mounting errors is analyzed. Second, reasonable characterization models for these error sources are established using homogeneous transformation matrices. Third, based on the abovementioned error models, a new rotor assembly error prediction algorithm is constructed. It is highly consistent with the actual connection processes. Finally, verification experiments are conducted. The experimental results show that deviation rates of the average values of six types of assembly errors relative to the predictions are all lower than 14%. The proposed prediction method has acceptable accuracy and practical significance.